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Copyright 1999-2013 by Genome Research Limited This document describes release 1 o! "rtemis a #$" se%uence &ie'er and se%uence annotation tool( "rtemis is !ree so!t'are) you can redistribute it and*or modi!y it under the terms o! the G$+ General ,ublic License as published by the -ree .o!t'are -oundation) either &ersion 2 o! the License/ or 0at your option1 any later &ersion( This program is distributed in the hope that it 'ill be use!ul/ but 23T45+T "$6 2"RR"$T6) 'ithout e&en the implied 'arranty o! 78RC4"$T"93L3T6 or -3T$8.. -5R " ,"RT3C+L"R ,+R,5.8( .ee the G$+ General ,ublic License !or more details( 6ou should ha&e recei&ed a copy o! the G$+ General ,ublic License along 'ith this program) i! not/ 'rite to the -ree .o!t'are -oundation/ 3nc(/ 9 Temple ,lace/ .uite 330/ 9oston/ 7" 02111-130: +." -or the !ull te;t o! the license see the section called Copyright Notice in Chapter 1(
Table of Contents 1( 3ntroduction to "rtemis 2hat is "rtemis< .ystem Re%uirements Getting and 3nstalling "rtemis 3nstalling =a&a 3nstallation 3nstructions !or +$3> and G$+*Linu; 3nstallation 3nstructions !or 7ac5.> 3nstallation 3nstructions !or 2indo's .e%uence and "nnotation -ile -ormats Concepts The ?8ntry? 879L*Genban@ -eatures 879L*Genban@ -eature Aeys 879L*Genban@ -eature Buali!iers ?Tab? -iles or ?Table? -iles The "cti&e 8ntries The #e!ault 8ntry -eature .egments The .election -eature Colours Contributions and .uggestions #istribution Conditions and "c@no'ledgments Copyright $otice 2( .tarting "rtemis Running "rtemis on +$3> and G$+*Linu; .ystems +$3> Command Line "rguments !or "rtemis -quiet -options -Xmsn -Xmxn -Dblack_belt_mode=false -Doffset=10000 -Duserplot=pathToFile -Dloguserplot=pathToFile
-Dbam=pathToFile -Dbam1=pathToFile1 -Dbam =pathToFile -Dbam!lone=n -Dchado="hostname#port$database%username" -Dread_onl& -Dsho'_for'ard_lines=false -Dsho'_re(erse_lines=false Running "rtemis on 7acintosh .ystems Running "rtemis on 2indo's .ystems The "rtemis Launch 2indo' The -ile 7enu The 5ptions 7enu 3( The "rtemis 7ain 2indo' 5&er&ie' o! the 8ntry 8dit 2indo' " brea@do'n o! the main "rtemis edit 'indo' The -ile 7enu .ho' -ile 7anager ((( Read "n 8ntry ((( Read 8ntry 3nto Read 9"7 * CC- ((( .a&e #e!ault 8ntry .a&e "n 8ntry .a&e "n 8ntry "s .a&e "ll 8ntries 2rite Clone This 2indo' .a&e "s 3mage -iles 0png*s&g1 ,rint ,rint ,re&ie' ,re!erences Close The 8ntries 7enu .et $ame 5! 8ntry .et #e!ault 8ntry Remo&e "n 8ntry Remo&e "cti&e 8ntries #eacti&ate "ll 8ntries The .elect 7enu -eature .elector ((( "ll "ll 9ases .elect "ll -eatures in $on-matching Regions $one 9y Aey C#. -eatures .ame Aey 5pen Reading -rame -eatures 5&erlapping .election 9ase Range ((( -eature "" Range ((( Toggle .election The Cie' 7enu .elected -eatures .election .earch Results C#. Genes "nd ,roducts
-eature -ilters 5&er&ie' -or'ard .trand 5&er&ie' Re&erse .trand 5&er&ie' -eature 9ases -eature 9ases "s -".T" -eature "mino "cids -eature "mino "cids "s -".T" -eature .tatistics -eature ,lots The Goto 7enu $a&igator ((( .tart o! .election 8nd o! .election -eature .tart -eature 8nd .tart o! .e%uence 8nd o! .e%uence -eature 9ase ,osition ((( -eature "mino "cid ((( The 8dit 7enu +ndo Redo .elected -eatures in 8ditor .ubse%uence 0and -eatures1 -ind 5r Replace Buali!ier Te;t Buali!ier0s1 o! .elected -eature .elected -eature0s1 7o&e .elected -eatures To Copy .elected -eatures To Trim .elected -eatures 8;tend .elected -eatures -i; .top Codons "utomatically Create Gene $ames -i; Gene $ames 9ases Contig Reordering ((( 4eader 5! #e!ault 8ntry The Create 7enu $e' -eature -eature -rom 9ase Range 3ntergenic -eatures -eatures -rom $on-matching Regions $e' 8ntry 7ar@ 5pen Reading -rames ((( 7ar@ 8mpty 5R-s ((( 7ar@ 5pen Reading -rames 3n Range ((( 7ar@ -rom ,attern ((( 7ar@ "mbiguities The Run 7enu Con!iguring the Run 7enu The Graph 7enu 4ide "ll Graphs "dd +sage ,lots ((( "dd +ser ,lot ((( GC Content 0D1
GC Content 0D1 2ith 2( .# Cuto!! "G Content 0D1 GC -rame ,lot Correlation .cores Re&erse Correlation .cores GC #e&iation 0G-C1*0GEC1 "T #e&iation 0"-T1*0"ET1 Aarlin .ignature #i!!erence Cumulati&e "T .@e' and Cumulati&e GC .@e' ,ositional "symmetry 3n!ormational 8ntropy .caled Chi .%uare 7utational Response 3nde; 8!!ecti&e Codon $umber 3ntrinsic Codon #e&iation 3nde; The #isplay 7enu .ho' 8ntry 9uttons .ho' 9ase Cie' .ho' -eature List The 8ntry 9utton Line The 5&er&ie' and #$" Cie's Changing the .election !rom a Cie' 2indo' 5ther 7ouse Controlled -unctions The ,op-up 7enu .crolling The Cie' Changing The .cale ?#irect 8diting? The -eature List Changing the .election !rom the -eature List 5ther 7ouse Controlled -unctions The ,op-up 7enu .crolling The List Graphs and ,lots $otes on +sing The 7ouse F( ,roGect -ile 7anager 5&er&ie' +sing the ,roGect -ile 7anager ( .ecure .hell 0..41 ,lugin To "rtemis 5&er&ie' o! the ..4 ,lugin Login 3n .etting up a ..4 tunnel +sing ,utty to .et +p " Tunnel +sing the ..4 connection to run -asta and 9L".T Con!iguring .earches to be run &ia ..4 H( "rtemis Con!iguration 5ptions The 5ptions -ile "rtemis 5ption #escriptions font_si)e font_name base_plot_height feature_plot_height dra'_feature_borders sho'_for'ard_lines sho'_re(erse_lines dra'_feature_arro's o(er(ie'_feature_labels o(er(ie'_one_line_per_entr&
sho'_list sho'_base_(ie' features_on_frame_lines frame_line_features feature_labels one_line_per_entr& genetic_codes translation_table_1 extra_ke&s extra_qualifiers common_ke&s h&perlinks undo_le(els minimum_orf_si)e direct_edit feature_dna_programs feature_protein_programs ncbi_dna_search ncbi_protein_search .etting Colours 5ptions -or ,lots and Graphs 5ptions -or " Chado #atabase 5ptions -ile -ormat "n 8;ample 5ptions -ile List of Tables 3-1( 3+9 9ase Codes
System Re uirements
"rtemis 'ill run on any machine that has a recent &ersion o! =a&a( This &ersion o! "rtemis re%uires =a&a 1(H at least( 7ost o! the de&elopment has been done using =#A &1(H and some o! the more ad&anced !eatures 09amCie' and CC-*9C- Cie'1 re%uire =a&a 1(H or higher( .ee the section called Getting and
Installin" #a$a
9e!ore installing "rtemis you 'ill need to ma@e sure you ha&e =a&a installed( Linu;/ +$3> users should get the current =a&a &ersion !rom the 5racle( 2indo's users should get latest stable release !rom =a&a &ersion !rom 5racle( 5n some &ersions o! 2indo's 0such as 2indo's 20001 you 'ill need be ha&e administrator pri&ileges !or your machine to success!ully install =a&a( 7acintosh users 'ith 7ac5. > should ha&e =a&a installed( 6ou can get the latest =a&a 1(H &ersion !rom "pple( =a&a : !or 3ntel 7ac running 7ac 5.> 10(:(3 or abo&e can be do'nloaded !rom 5racle(
The uncompressed dis@ image !ile ?artemisKact(dmg? can be mounted by double clic@ing on it( The mounted image/ ?artemisKact?/ can then be opened and the so!t'are contents displayed by double clic@ing on it( 5pen an read the ?Readme(t;t? !ile(
" drop do'n menu o! the se%uences in the 8ntry toolbar 0see the section called A
brea)do(n of the main Artemis edit (indo( in Chapter 31 at the top can then used to select the se%uence to &ie'( 3nde;ed G--3 !ormat( This can be read in and o&erlaid onto an inde;ed -".T" !ile( The inde;ed G--3 !ile contains the !eature annotations( To inde; the G-- !irst sort and bgIip the !ile and then use tabi; 'ith ?-p g!!? option 0see the tabi; manual1J
,grep -"." in+gff/ grep -( -"." in+gff 0 sort -k111 -k212n3 0 bg)ip 4 sorted+gff+g)/ tabix -p gff sorted+gff+g)
" drop do'n menu o! the se%uences in the 8ntry toolbar 0see the section called A brea)do(n of the main Artemis edit (indo( in Chapter 31 at the top can then used to select the se%uence to &ie'( +sing inde;ed -".T" and inde;ed G-- !iles impro&es the memory management and enables large genomes to be &ie'ed( $ote that as it is inde;ed the se%uence and annotation are read-only and cannot be edited( 2hen there are many contigs to select !rom it can be easier to display the one o! interest by typing the name into the drop do'n list( The output o! MS/crunch( MS/crunch must be run 'ith the 0) or 0d !lags( The output o! blastall &ersion 2(2(2 or better( blastall must be run 'ith the 0m 1 !lag 'hich generates one line o! in!ormation per 4.,( $ote that currently "rtemis displays each 9last 4., as a separate !eature rather than displaying each 9L".T hit as a !eature(
Concepts
4ere are some general concepts about "rtemis that may ma@e the rest o! this manual clearer(
The 23ntry2
"n ?entry? in "rtemis-spea@ is not necessarily a complete 879L or G8$9"$A entry( 3n most places in this manual 'hen 'e re!er to an entry 'e mean a !ile that contains Gust the !eature table lines 0the FT lines1 o! an 879L*G8$9"$A entry 0see the section called *+ab* ,iles or *+able* ,iles1( "!ter loading a se%uence and opening an entry edit 'indo' 0see the section called Open ... in Chapter 21 it is then possible to o&erlay many !eature tables 0see the section called Read An Entry ... in Chapter 31( 8ach o! these !eature table !iles is called an entry by "rtemis and itMs !eatures are @ept separate !rom those o! other entries( This meaning o! the 'ord ?entry? is used by most o! the items in the -ile menu 0see the section called +he ,ile -en in Chapter 31 and by the items in the 8ntry menu 0see the section called +he Entries -en in Chapter 31(
3M4L(!enban5 .eatures
" ?!eature? in an 879L or Genban@ !ile is a region o! #$" that has been annotated 'ith a @ey*type 0see the section called E-B$#Genban) ,eat re .eys 1 and Iero or more %uali!iers 0see the section called
E-B$#Genban) ,eat re / alifiers 1( 3n an 879L or Genban@ !ormated !ile the !eatures o! a piece o! #$" are listed in the !eature table section 0see the section called *+ab* ,iles or *+able* ,iles1(
.eature Se"ments
The term ?segment? in the conte;t o! a C#. !eature means ?e;on?( 2e use the term ?segment?/ because non-C#. !eatures 0such as miscK!eature1 can ha&e e;on-li@e parts too/ but the term ?e;on? 'ould be inappropriate in that case(
The Selection
3n common 'ith applications li@e 'ord processors and graphics programs/ "rtemis allo's the user to ?select? the obGects that the program 'ill act on( The obGects to act on in "rtemis are !eatures/ !eature segments or bases( 3! a !eature segment is added to the selection/ the !eature that contains the segment is implicitly added as 'ell( The current selection can be changed 'ith the .elect 7enu 0see the section called +he &elect -en in Chapter 31 or using the mouse 0see the section called Changing the &election from a 0ie( 'indo( in Chapter 3 and the section called Changing the &election from the ,eat re $ist in Chapter 31(
.eature Colours
8ach !eature displayed in "rtemis can be gi&en a colour( The a&ailable colours are set in the options !ile 0see Chapter H1 and are assigned to a !eature by adding a $colour %uali!ier 0see the section called &elected ,eat res in Editor in Chapter 31( Currently there are t'o 'ays o! speci!ying !eature colours( The !irst 'ay uses a single number( -or e;ample red is colour 2/ so adding $colour= as a !eature %uali!ier 'ill ma@e that !eature red( The second 'ay is to speci!y the red/ green and blue components o! the colour( 8ach o! the components can ta@e &alues !rom 0 to 2 / 'ith 2 being the most intense( -or e;ample $colour= 88 0 0 is another 'ay to gi&e a !eature the colour red( 3! no $colour %uali!ier is set !or a !eature a de!ault colour is used 0the de!ault colours are also speci!ied in the options !ile1(
Copyri"ht &otice
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=<D75T=7A;T< TL< @=K9=>6 >5 @<=67TT<D >AKB<1 A< ?7>A?< TK IK; FK= D>6>9<51 7:!?;D7:9 >:I 9<:<=>?1 5@<!7>?1 7:!7D<:T>? K= !K:5<P;<:T7>? D>6>9<5 >=757:9 K;T KF TL< ;5< K= 7:>A7?7TI TK ;5< TL< @=K9=>6 ,7:!?;D7:9 A;T :KT ?767T<D TK ?K55 KF D>T> K= D>T> A<7:9 =<:D<=<D 7:>!!;=>T< K= ?K55<5 5;5T>7:<D AI IK; K= TL7=D @>=T7<5 K= > F>7?;=< KF TL< @=K9=>6 TK K@<=>T< J7TL >:I KTL<= @=K9=>6531 <B<: 7F 5;!L LK?D<= K= KTL<= @>=TI L>5 A<<: >DB75<D KF TL< @K557A7?7TI KF 5;!L D>6>9<5+
-quiet
This option tells "rtemis to suppress normal in!ormational messages 'hile running(
-options
This option instructs "rtemis to read an e;tra !ile o! options a!ter reading the standard options( 0.ee the section called +he Options ,ile in Chapter H !or more about the "rtemis options !ile(1 -or e;ample -options +$ne'_options 'ill instruct "rtemis to read ne'_options in the current directory as an options !ile(
-Xmsn -Xmxn
+se -Xmsn to speci!y the initial siIe/ in bytes/ o! the memory allocation pool( This &alue must be a multiple o! 102F greater than 179( "ppend the letter @ or A to indicate @ilobytes/ or m or 7 to indicate megabytes( +se -Xmxn to speci!y the ma;imum siIe/ in bytes/ o! the memory allocation pool( This &alue must a multiple o! 102F greater than 279( "ppend the letter @ or A to indicate @ilobytes/ or m or 7 to indicate megabytes(
-Dblack_belt_mode=false
3! this is set to !alse then 'arning messages are @ept to a minimum(
-Doffset=10000
This sets the base position that "rtemis opens at/ e(g( 10000(
-Duserplot=pathToFile
This can be used to open userplots !rom the command line( The paths are comma separated to open multiple plots 0-#userplotOM*pathTo-ile*user,lot1/*pathTo-ile*user,lot2M1(
-Dloguserplot=pathToFile
This is the same as the abo&e userplot option e;cept that the log trans!orm o! the data is plotted(
-Dbam=pathToFile
This can be used to open 9"7 !iles and*or CC-*9C- !iles 0see the section called Read BA- # 0C, ... in Chapter 3 !or more about the using these !ile types1( This can ta@e a path name to a !ile or an 4TT, address(
-Dbam!lone=n
7ultiple 9"7 panels can be opened using the bamClone !lag this is used 'ith the -#bam !lagJ art 08bamDE(pathTo.ile(file1.bamF(pathTo.ile(file9.bamE 08bamCloneDn 0'here n is an integer greater than 11( "ll 9"7 !iles are then sho'n in each panel(
-Dchado="hostname#port$database%username"
This is used to get "rtemis to loo@ !or the database( The address o! the database 0hostname/ port and name1 can be con&eniently included 0e(g( -#chadoO?genedb-db(sanger(ac(u@J F32*snapshot<genedbKro?1 and these details are then the de!ault database address in the popup login 'indo'(
-Dread_onl&
-or a read only chado connection -#readKonly is speci!ied on the command line 0e(g( art
-Dsho'_for'ard_lines=false
4ide*sho' !or'ard !rame lines(
-Dsho'_re(erse_lines=false
4ide*sho' re&erse !rame lines(
Changing the &alue a!ter ->m; 'ill change the memory used by "rtemis(
The Artemis Launch WindoThis is the !irst 'indo' that opens 'hen you start "rtemis( The menus at the top o! this 'indo' allo' you to read a ne' se%uence or embl entry(
,pen ...
3! you select this menu item a !ile re%uester 'ill be displayed 'hich allo's you to open a !lat !ile containing an entry( 3! the !ile you select is success!ully read a ne' 'indo' 'ill open/ 'hich sho's the se%uence and !eatures !or the entry( .ee Chapter 3 to !ind out ho' to use the main 'indo'(
7uit
This menu item 'ill close all 'indo's and then e;it the program
Sho- Lo" Windo.ho' the log o! in!ormational messages !rom "rtemis( Currently the log 'indo' is only used on +$3> and G$+*Linu; systems to sho' the output o! e;ternal programs( This menu item is only a&ailable 'hen running "rtemis on +$3> or G$+*Linu; systems( The logging is controlled by logFG( The logFG(properties !ile 0etc*logFG(properties in the source distribution1 sets the le&el o! logging( This can be used to send the logging in!ormation to other places such as a !ile(
Gide Lo" Windo4ide the log o! in!ormational messages( This menu item is only a&ailable 'hen running "rtemis on +$3> or G$+*Linu; systems(
Chapter ?. The Artemis Main Windo,$er$ie- of the 3ntry 3dit WindoThis 'indo' is the main editing and &ie'ing 'indo'( .ee the section called Open ... in Chapter 2 or the section called Open from EBI - Dbfetch ... in Chapter 2 to !ind out ho' to read an entry 0and hence open one o! these 'indo's1( The !ollo'ing images sho' a brea@do'n o! the main "rtemis edit 'indo'( The !ull screen shot is here(
F(
H( AeyJ 1( The menus !or the main 'indo' 0described later in this chapter1( 2( " one line summary o! the current selection 0see the section called +he &elect -en and the section called +he &election in Chapter 1 !or more1( 3( This line contains one button !or each entry that has been loaded( These buttons allo' the user to set the de!ault entry 0see the section called +he Defa lt Entry in Chapter 11 and to set the acti&e entries 0see the section called +he Acti2e Entries in Chapter 11( -or more detail on operating the buttons see the section called +he Entry B tton $ine( F( This sho's an o&er&ie' o! the se%uence and the !eatures !rom the acti&e entries( 0see the section
called +he O2er2ie( and DNA 0ie(s1( ( This is called the ?#$" &ie'? to distinguish it !rom the o&er&ie'/ but in !act it operates in a &ery similar 'ay( 0see the section called +he O2er2ie( and DNA 0ie(s1( H( " te;tual summary o! the acti&e !eatures( 0.ee the section called +he ,eat re $ist1(
mappings to a re!erence se%uence( 7ultiple 9"7 !iles can be loaded in !rom here either by selecting each !ile indi&idually or by selecting a !ile o! path names to the 9"7 !iles( The 9"7 !iles can be read !rom a local !ile system or remotely !rom an 4TT, ser&er( 9amCie' 'ill loo@ to match the length o! the se%uence in "rtemis 'ith the re!erence se%uence lengths in the 9"7 !ile header( 3t 'ill display a 'arning 'hen it opens i! it !inds a matching re!erence se%uence 0!rom these lengths1 and changes to displaying the reads !or that( The re!erence se%uence !or the mapped reads can be changed manually in the drop do'n list in the toolbar at the top o! the 9amCie'( 3n the case 'hen the re!erence se%uences are concatenated together into one 0e(g( in a multiple -".T" se%uence1 and the se%uence length matches the sum o! se%uence lengths gi&en in the header o! the 9"7/ "rtemis 'ill try to match the names 0e(g( locusKtag or label1 o! the !eatures 0e(g( contig or chromosome1 against the re!erence se%uence names in the 9"7( 3t 'ill then adGust the read positions accordingly using the start position o! the !eature( 2hen open the 9amCie' can be con!igured &ia the popup menu 'hich is acti&ated by clic@ing on the 9amCie' panel( The MCie'M menu allo's the reads to be displayed in a number o! &ie'sJ stac@/ strandstac@/ paired-stac@/ in!erred siIe and co&erage( 3n "rtemis the 9amCie' display can be used to calculate the number o! reads mapped to the regions co&ered by selected !eatures( 3n addition the reads per @ilobase per million mapped reads 0R,A71 &alues !or selected !eatures can be calculated on the !ly( $ote this calculation can ta@e a 'hile to complete( Cariant Call -ormat 0CC-1 !iles can also be read( The CC- !iles need to be compressed and inde;ed using bgIip and tabi; respecti&ely 0see the tabi; manual and do'nload page1( The compressed !ile gets read in 0e(g( !ile(&c!(gI1 and belo' are the commands !or generating this !rom a CC- !ileJ
bg)ip file+(cf tabix -p (cf file+(cf+g)
"lternati&ely a 9inary CC- 09C-1 can be inde;ed 'ith 9C-tools and read into "rtemis or "CT( "s 'ith reading in multiple 9"7 !iles/ it is possible to read a number o! 0compressed and inde;ed1 CC!iles by listing their !ull paths in a single !ile( They then get displayed in separate ro's in the CC- panel(
-or single base changes the colour represents the base it is being changed to/ i(e( T blac@/ G blue/ " green/ C red( There are options a&ailable to !ilter the display by the di!!erent types o! &ariants( Right clic@ing on the CC- panel 'ill display a pop-up menu in 'hich there is a M-ilter(((M menu( This opens a 'indo' 'ith chec@ bo;es !or a number o! &araint types and properties that can be used to !ilter on( This can be used to sho' and hide synonymous/ non-synonymous/ deletion 0grey1/ insertion 0magenta1/ and multiple allele 0orange line 'ith a circle at the top1 &ariants( 3n this 'indo' there is a chec@ bo; to hide the &ariants that do not o&erlap C#. !eatures( There is an option to mar@ &ariants that introduce stop codons 0into the C#. !eatures1 'ith a circle in the middle o! the line that represents the &ariant( There are also options to !ilter the &ariants by &arious properties such as their %uality score 0B+"L1 or their depth across the samples 0#,1( ,lacing the mouse o&er a &ertical line sho's an o&er&ie' o! the &ariation as a tooltip( "lso right clic@ing o&er a line then gi&es an e;tra option in the pop-up menu to sho' the details !or that &ariation in a separate 'indo'( There are also alternati&e colouring schemes( 3t is possible to colour the &ariants by 'hether they are synonymous or non-synonymous or by their %uality score 0the lo'er the %uality the more !aded the &ariant appears1( There is an option to pro&ide an o&er&ie' o! the &ariant types 0e(g( synonymous/ non-synonymous/ insertion/ deletion1 !or selected !eatures( "lso/ !iltered data can be e;ported in CC- !ormat/ or the reconstructed #$" se%uences o! &ariants can be e;ported in -".T" !ormat !or selected !eatures or regions !or !urther analyses( These se%uences can be used as input !or multiple se%uence alignment tools(
Sa$e An 3ntry
This item 'ill do the same as ?.a&e #e!ault 8ntry? !or the chosen entry(
Sa$e An 3ntry As
This sub-menu contains the less !re%uently used sa&e !unctions(
&e- .ile
"s@ !or the name o! !ile to sa&e the gi&en entry to( The name o! entry 0as displayed in the entry button line1 'ill change to the ne' name(
3M4L .ormat
This does the same as ?.a&e "n 8ntry "s -R $e' -ile (((?/ but 'ill 'rite the !eatures and se%uence o! the entry in 879L !ormat( $ote that currently the header o! a G8$9"$A entry canMt be con&erted to the e%ui&alent 879L header 0it 'ill be discarded instead1(
!3&4A&6 .ormat
This does the same as ?.a&e "n 8ntry "s -R $e' -ile (((?/ but 'ill 'rite the !eatures and se%uence o! the entry in G8$9"$A !ormat( $ote that currently the header o! a 879L entry canMt be con&erted to the e%ui&alent G8$9"$A header 0it 'ill be discarded instead1(
!.. .ormat
2rites the !eatures in G-- !ormat and se%uence o! the entry in -".T" !ormat to a !ile selected by the user( $ote that i! you use this !unction on an 879L or G8$9"$A entry the header 'ill discarded(
Write
4ases ,f Selection
,rompt !or a !ile name and then 'rite the bases o! the selection to that !ile in the selected !ormat( 3! the selection consists o! !eatures 0rather than a base range1 then the bases o! each !eature 'ill be 'ritten to the !ile as a separate record( 3! the selection is a range o! bases/ then those bases 'ill be 'ritten(
All 4ases
,rompt !or a !ile name/ then 'rite the complete se%uence to that !ile in the selected !ormat(
Clone This Windo7a@e a ne' main 'indo' 'ith the same contents as the current 'indo'( "ll changes in the old 'indo' 'ill be re!lected in the ne' 'indo'/ and &ice &ersa( The e;ception to this rule is the selection 0see the section called +he &election in Chapter 11/ 'hich is not shared bet'een the old and ne' 'indo'(
/rint
This option can be used to print the contents o! the current 'indo' to a !ile as ,ost.cript or to a printer(
/rint /re$ieThis opens the print image in a pre&ie' 'indo'( This sho's 'hat the image 'ill loo@ li@e 'hen printed to a !ile(
/references
This enables the user to de!ine their o'n shortcut pre!erences(
Close
Close this 'indo'(
Remo$e An 3ntry
Remo&e an entry !rom "rtemis by choosing one o! the entries !rom the sub-menu( The original !ile that this entry came !rom 0i! any1 'ill not be remo&ed(
!or details1((
All
Reset the selection so that nothing is selected then select all the !eatures in the acti&e entries( Pshortcut @eyJ "Q
All 4ases
Reset the selection so that nothing is selected then select all the bases in the se%uence(
&one
Clear the selection so that nothing is selected( Pshortcut @eyJ $Q
4y 6ey
"s@ the user !or a !eature @ey/ reset the selection so that nothing is selected/ then select all the !eatures 'ith the @ey gi&en by the user(
C8S .eatures
Reset the selection so that nothing is selected/ then select all the C#. !eatures that do not ha&e a *pseudo %uali!ier(
Same 6ey
.elect all the !eatures that ha&e the same @ey as any o! the currently selected !eatures(
To""le Selection
3n&ert the selection - a!ter choosing this menu item the selection 'ill contain only those !eatures that 'ere not in the selection be!orehand(
Selected .eatures
5pen a &ie' 'indo' !or each selected !eature sho'ing itMs !eature table entry( Pshortcut @eyJ CQ
Selection
5pen a &ie' 'indo' that 'ill sho' the current selection( The 'indo' is updated as the selection changes/ so it can be le!t open( 2hen one !eature is selected the 'indo' 'ill sho' the te;t 0879L/ Gen9an@ or G-- !ormat1 o! the !eature/ the base composition/ GC percentage/ correlation score 0see the section called Correlation
&cores1/ and the bases and translation o! the se%uence o! the !eature( 2hen t'o or more !eatures are selected the 'indo' 'ill sho' the te;t 0879L/ Gen9an@ or G-- !ormat1 o! the !eatures/ the base composition/ a&erage GC percentage/ a&erage correlation score/ minimum*ma;imum GC content and minimum*ma;imum correlation score o! the !eature se%uence( 2hen a range o! bases is selected the 'indo' 'ill sho' the base composition/ GC content percentage and the bases and translation o! the se%uence o! the !eature(
Search Results
5n this sub-menu allo's the user to &ie' the results o! !eature searches that are launched !rom the run menu in "rtemis 0see the section called +he R n -en 1(
.eature .ilters
8ach o! the items in this sub-menu each allo' the user to &ie' a subset o! the acti&e !eatures( "n e;ample o! a subset is all those !eatures 'ith misc_feature as a @ey( The !eatures are displayed in a ne' 'indo' that contains a menu bar 'ith possible actions to apply to the subset/ and !eature list 0see the section called +he ,eat re $ist1( 7ost o! the possible actions 'ill apply only to the !eatures in the list( -or e;ample ?.ho' 5&er&ie'? in the Cie' menu 0see the section called O2er2ie(1 'ill include statistics only on the !eatures in the list(
,$er$ie5pen a ne' 'indo' the 'ill sho' a summary o! the acti&e entries and some statistics about the se%uence 0such as the GC content1( Pshortcut @eyJ 5Q
Se uence Statistics
The o&er&ie' 'indo' sho' the !ollo'ing statistics about the se%uenceJ $umber o! bases(
GC percentage( The number o! each nucleotide in the se%uence( GC percentage o! non-ambiguous bases - ie( the GC content percentage ignoring bases other than "/T/C and G( This should be the same as the ?GC percentage? abo&e(
.eature Statistics
The o&er&ie' 'indo' also sho's the !ollo'ing statistics about the !eatures in the acti&e entries 0i! there are any !eatures1( $ote that the ?genes? are the non-pseudo C#. !eatures( $umber o! !eatures in the acti&e entries 0see the section called +he Acti2e Entries in Chapter 11( Gene density - the a&erage number o! non-pseudo C#. !eatures per 1000 bases( "&erage gene length - the a&erage length o! non-pseudo C#. !eatures 0not including introns1( $umber o! non-spliced genes( $umber o! spliced genes( $umber o! pseudo genes 0ie( C#. !eatures 'ith a *pseudo %uali!ier1( ,rotein coding 0C#.1 !eatures( ,rotein coding 0C#.1 bases( ,rotein coding percentage - ie( the number o! coding bases e;cluding introns( Coding percentage 0including introns1( " summary o! the number o! !eatures o! each @ey 0type1 and their colours(
.or-ard Strand ,$er$ie5pen a ne' 'indo' the 'ill sho' a summary o! the !eatures and bases o! the !or'ard strand(
Re$erse Strand ,$er$ie5pen a ne' 'indo' the 'ill sho' a summary o! the !eatures and bases o! the re&erse strand(
.eature 4ases
Create a &ie' 'indo' !or each selected !eature/ 'hich sho's bases o! the !eature(
.eature Statistics
.ho' some statistics about each selected !eature( 5n the le!t on the !eature in!ormation 'indo' is the amino acid composition o! the !eature( 5n the right is the codon composition o! the !eature(
.eature /lots
5pen a 'indo' !or each selected !eature that sho's a plot o! the Ayte-#oolittle 4ydrophobicity Pshort nameJ h&drophobicit&Q/ the 4opp-2oods 4ydrophilicity Pshort nameJ h&drophilicit&Q/ and an appro;imation o! the GCG Coiled Coils algorithm Pshort nameJ coiled_coilQ( 0-or more detail about the coiled coils algorithm see ?,redicting Coiled Coils !rom ,rotein .e%uences?/ .cience Col( 2 2 page 11H2(1 Pshortcut @eyJ 2Q .ome general in!ormation about graphs and plots in "rtemis can be !ound in the section called Graphs and 1lots( Con!iguration options !or graphs are described in the section called Options ,or 1lots and Graphs in Chapter H(
&a$i"ator ...
5pen a ne' na&igation 'indo'( Pshortcut @eyJ GQ This 'indo' allo's the user to per!orm !i&e di!!erent tas@sJ 1( Scroll all the $ie-s so that a particular base is in the centre of the display . To use this !unction/ type a base position into the bo; to the right o! the ?Goto 9aseJ? label then press the goto button at the bottom o! the 'indo'( The re%uested base 'ill be selected and then the o&er&ie' display and the #$" display 'ill scroll so that the base is as near as possible to the middle o! the main 'indo'( 2( .ind the ne)t feature that has the "i$en "ene name . To use this !unction/ type a gene name into the bo; to the right o! the ?Goto -eature 2ith This Gene $ameJ? label and then press the goto button( "rtemis 'ill select the !irst !eature 'ith the gi&en te;t in any o! itMs %uali!iers and 'ill then scroll the display so that !eature is in &ie'( 3( .ind the ne)t feature that has a ualifier containin" a particular strin" . To use this !unction/ type a string into the bo; to the right o! the ?Goto -eature 2ith This Buali!ier CalueJ? label and then press the goto button( "rtemis 'ill select the !irst !eature 'ith the gi&en string in any o! itMs %uali!ier &alues 0see the section called E-B$#Genban) ,eat re / alifiers in Chapter 11 and 'ill then scroll the display so that !eature is in &ie'( F( .ind the ne)t feature that has a particular 5ey . To use this !unction/ type a @ey into the bo; to the right o! the ?Goto -eature 2ith This AeyJ? label and then press the goto button( "rtemis 'ill select the !irst !eature 'ith the gi&en @ey and 'ill then scroll the display so that !eature is in &ie'( ( .ind the ne)t occurrence of a particular base pattern in the se uence . To use this !unction/ type a base pattern into the bo; to the right o! the ?-ind 9ase ,atternJ? label and then press the goto button( "rtemis 'ill select the !irst contiguous group o! bases on either strand that match the gi&en base pattern and 'ill then scroll the display so that those bases are in &ie'( "ny 3+9 base code can be used in the pattern/ so !or e;ample searching !or aanntt 'ill match any si; bases that start 'ith ?aa? and ends 'ith ?tt?( .ee Table 3-1 !or a list o! the a&ailable base codes( H( .ind the ne)t occurrence of a particular residue pattern in the se uence . To use this !unction/ type a amino acid pattern into the bo; to the right o! the ?Goto "mino "cid .tringJ? label and then press the goto button( "rtemis 'ill select the !irst contiguous group o! bases on either strand that translate to the gi&en amino acids and 'ill then scroll the display so that those bases are in &ie'( The letter M>M can be used as an ambiguity code/ hence M"">>>##M 'ill match M""LRT##M or M""TTT##M etc( $ote that !or all the !unctions abo&e e;cept the !irst 0?Goto 9ase?1/ i! the ?.tart search at beginning? option is set or i! there is nothing selected the search 'ill start at the beginning o! the se%uence( 5ther'ise the search 'ill start at the selected base or !eature( This means that the user can step through the matching bases or !eatures by pressing the goto button repeatedly( 3! the ?3gnore Case? toggle is on 0'hich is the de!ault1 "rtemis 'ill ignore the di!!erence bet'een upper and lo'er case letters 'hen searching !or a gene name/ a %uali!ier &alue or a !eature @ey( The ?"llo' .ubstring 7atches? toggle a!!ects 2 and 3( 3! on "rtemis 'ill search !or %uali!ier &alues that contain the gi&en characters( -or e;ample searching !or the genename C#C 'ill !ind C#C1/ C#C2/ "9C#C etc( 3! the toggle is o!! "rtemis 'ill only !ind e;act matches/ so searching !or the gene C#C 'ill only !ind !eatures that ha&e $gene="!D!" not $gene="!D!11"(
Start of Selection
.croll all the &ie's so that the !irst base o! the selection is as close to the centre as possible( 3! the a range o! bases is selected the &ie's 'ill mo&e to the !irst base o! the range( 3! one or more !eatures are selected/ then the !irst base o! the !irst selected !eature 'ill be centred( 5ther'ise/ i! one or more segments 0see the section called ,eat re &egments in Chapter 11 is selected then the !irst base o! the !irst selected segment 'ill be centred( Pshortcut @eyJ control-le!tQ
3nd of Selection
This does the same as ?Goto .tart o! .election?/ but uses the last base o! the selected range or the last base o! the last selected !eature or segment( Pshortcut @eyJ control-rightQ
.eature Start
.croll the &ie's to the start o! the !irst selected !eature(
.eature 3nd
.croll the &ie's to the end o! the !irst selected !eature(
Start of Se uence
.croll the &ie's so that the start o! the se%uence is &isible( Pshortcut @eyJ control-upQ
3nd of Se uence
.croll the &ie's so that the end o! the se%uence is &isible( Pshortcut @eyJ control-do'nQ
%ndo
This !unction 'ill undo the last change that 'as made using the 8dit or Create menus( +p to 20 changes can be undone( This menu item is only enabled 'hen there is something to undo( This limit can be changed in the options !ile 0see the section called undo_levels in Chapter H1( Pshortcut @eyJ +Q
Redo
This !unction 'ill redo the last undo operation(
-rom the top do'n the edit 'indo' has these partsJ 1( "t the top le!t is a selector !or choosing the @ey o! the !eature( This only contains a subset o! the legal @eys( The subset can be changed by changing the common_ke&s option in the options !ile 0see the section called common_keys in Chapter H1( "t the top right o! the edit 'indo' is a selector !or adding a %uali!ier( -or e;ample choosing note !rom the menu 'ill insert $note="" into the %uali!ier edit area( 2( =ust belo' the @ey and %uali!ier selector is the location entry !ield( "rtemis understands most o! the 879L location synta;/ including Goins/ complements/ ranges 'ith non-e;act ends 0eg( ,100+ 003++4F801 and re!erences to other entries 0eg( Moin,100++ 0015@A F>1#100++ 0031( 3( 9elo' the location is a ro' o! buttonsJ The !omplement button 'ill complement the contents o! the location !ield( The 9rab =ange button 'ill grab the currently selected range into the location !ield( The =emo(e =ange button 'ill remo&e the selected bases !rom the location string( This is normally used to create an intron in a !eature( ,ressing the 9oto Feature button has the same e!!ect as the ?.tart o! .election? item in the ?Goto? menu( 0.ee the section called &tart of &election !or more1( The 5elect Feature button selects this !eature 0in the same 'ay as clic@ing on the !eature in one o! the &ie's1(
F( The centre o! the edit 'indo' contains the %uali!ier entry section( The %uali!iers should be entered the in same 'ay the appear in the !eature table part o! an 879L entry/ but 'ithout the leading FT and spaces( ( The bottom o! the 'indo' contains three buttons( The KO button 'ill update the !eature 'ith the changes that ha&e been made by the user and 'ill then close the edit 'indo'( The !ancel button
'ill discard the changes and then close the 'indo'( The >ppl& 'ill ma@e the changes/ but 'ill not close the 'indo'( 9e!ore any changes are made the location and the %uali!iers are chec@ed !or !ormatting errors( "ny errors 'ill brought to the attention o! the user through the use o! annoying pop-up bo;es( $o changes 'ill be per!ormed until there all errors ha&e been !i;ed(
Remo$e ...
This !unction allo's the user to remo&e all %uali!iers 'ith a particular name !rom all the selected !eatures(
Con$ert ...
This !unction allo's the user to con&ert all %uali!iers o! a particular type to another %uali!ier !or all the selected !eatures(
Selected .eatureIsJ
8uplicate
7a@e a copy o! each selected !eature( 8ach ne' !eature 'ill be added Gust a!ter the original in the same entry as the original( Pshortcut @eyJ #Q
Mer"e
Create a ne' !eature that contains all the e;ons and %uali!iers o! the selected !eatures( The selected !eatures must all ha&e the same @ey( Pshortcut @eyJ 7Q
%nmer"e
3! the selection contains e;actly t'o e;ons and those e;ons are adGacent in the same !eature/ split the !eature into t'o pieces bet'een the e;ons( The original !eature is truncated and a ne' !eature is created( The %uali!iers o! the old !eature are copied to ne' !eature(
8elete
Remo&e each selected !eature !rom itMs entry( Pshortcut @eyJ control-deleteQ
8elete 3)ons
#elete the selected e;ons( The last e;on o! a !eature canMt be deleted 0delete the 'hole !eature instead1(
Remo$e Introns
#elete the selected introns(
To Any
This 'or@s in the same 'ay as ?Trim .elected -eatures To 7et?/ but 'ill attempt to mo&e the start position o! the !eature to the !irst TTG/ "TG or GTG in the !eature i! it does not already start on one o! those codons( "s abo&e it 'ill only search the !irst thirty percent o! the !eature bases and 'ill only search the !irst segment o! a multi-segment !eature(
To &e)t Met
-or each o! the selected !eatures this !unction 'ill attempt to mo&e the start position to the ne;t "TG in the !eature 0the !irst codon is s@ipped1( 3! there is no "TG in the !irst thirty percent o! the bases o! the !eature the start position 'ill be unchanged( The search 'ill stop at the end o! the !irst segment o! a multisegment !eature( Pshortcut @eyJ TQ
To &e)t Any
This 'or@s in the same 'ay as ?Trim .elected -eatures To $e;t 7et?/ but 'ill attempt to mo&e the start position o! the !eature to the ne;t TTG/ "TG or GTG in the !eature 0the !irst codon is s@ipped1( "s abo&e it 'ill only search the !irst thirty percent o! the !eature bases and 'ill only search the !irst segment o! a multi-segment !eature( Pshortcut @eyJ 6Q
4ases
Re$erse And Complement
Re&erse and complement the se%uence and all the !eatures in all the entries 0acti&e and inacti&e1(
&e- .eature
Create a ne' !eature in the de!ault entry 'ith a @ey o! ?miscK!eature? 0see the section called E-B$#Genban) ,eat re .eys in Chapter 11/ a location o! that spans the 'hole se%uence and 'hich has no %uali!iers 0see the section called E-B$#Genban) ,eat re / alifiers in Chapter 11(
Inter"enic .eatures
Create ne' !eatures bet'een C#. !eatures in the de!ault entry all 'ith the ?miscK!eature? @ey(
&e- 3ntry
Create a ne' entry 'ith no name and no !eatures( The ne' entry 'ill become the de!ault entry 0see the section called +he Defa lt Entry in Chapter 11(
Table ?01. I%4 4ase Codes R O " or G 6 O C or T A O G or T 7 O " or C . O G or C 2 O " or T 9 O C/ G or T # O "/ G or T C O "/ C or G
$ O "/ C/ G or T 4 O "/ C or T
Mar5 Ambi"uities
Create a ne' !eature !or each bloc@ o! ambiguous bases( The ne' !eatures 'ill ha&e a @ey o! misc_feature and 'ill created in a ne' entry called ?ambiguous bases?(
because the !ile name is stored in the entry you 'ill need to sa&e the entry to @eep the association bet'een the !eatures and the output !iles( F( " !ile is then 'ritten 0called something li@e blastp$file_of_filenames+11 that contains the names o! all the ne'ly created se%uence !iles in the blastp directory( ( "rtemis then tries to read the run_blastp script !rom the "rtemis installation directory( The script is e;ecuted li@e thisJ run_blastp blastp$file_of_filenames+1 SoptionsT 'here SoptionsT currently must be a single 'ord 0normally a database to search1( 3n the case o! blastp*blastn*!asta etc( the second argument o! the script is passed directly to the blast*!asta as the database name( -or testing purposes it is possible to run run_blastp on the command line 'ith the same arguments as abo&e( run_blastp 'ill run blastp on each o! the se%uence !iles listed in file_of_filenames+blastp and sa&e the output in the corresponding +out !ile( H( 3! the program is success!ully started/ control 'ill immediately return to the user( 2hen run_blastp !inishes a message 'ill be displayed to alert the user( 3! necessary/ it is possible to e;it once "rtemis indicates that the e;ternal program has been started and the entry has been sa&ed( run_blastp 'ill @eep running in the bac@ground(
>;; F8+0, 8 NFN3 >;! 1 +N, 1D0003 >;> 1F+1, 1DG N3 >;9 0+D, F1FGN3 9;; D+F, 220183 9;! 11+0, 1N2DG3 9;> 1 +F, 1E2813 9;9 E+F, 1 2 3
2( the !irst column corresponds to the base position and is an integer( $ote to distinguish this !ormat !rom the pre&ious !ormat the !irst line o! the !ile must start 'ith a MVM( Line colours can be speci!ied in the header using the @ey'ord colour !ollo'ed by space separated RJGJ9 &alues !or each line( The ne;t ro's0s1 are the data &alues( 8;ample e;tractJ
. A>5< B>?1 B>? B>?F B>?2 B>?8 B>?N . colour 8#180#88 88#0#0 0# 88#0 0#0# 88 100#100#100 80#180#80 1GN 02+E E2E+ F 0 0 0 8FN+02 GE E02+DD 0 EFG+ 0 NE1+NF 0 28 0 NDD+DE 0 0 0 81+1E 88F 0 0 0 0 0 8 +2 N82 0 0 0 0 FF2+ 0 NEN 0 0 N8 +GE 0 0 0 EF1 0 0 0 0 0 NG+DG +++
3( inde;ed tab delimited !ile( -or this tabi; is used 0see the tabi; manual1 to create an inde;( This is especially use!ul !or large data sets as it is memory e!!icient and only reads the data corresponding to the &isible region in "rtemis( The !irst columns contain the se%uence name and base position
and this is then !ollo'ed by the &alues to be plotted( -or e;ample M!ile(plotM is a tab delimited !ile 'ith column 1 containing the se%uence name and column 2 the positions/ this is sorted and then inde;ed 'ith tabi;J
,grep -"." file+plot/ grep -( -"." file+plot 0 sort -k111 -k 1 n3 0 bg)ip 4 sorted+plot+g) / tabix -s 1 -b -e sorted+plot+g)
8;ample e;tractJ
foo foo foo foo foo foo +++ 1 F 2 8 N 8 1 8 0 8 F0 8 10 1N F FN 1 1 1 1 1 1 D 2 D 2 1 2 8 1 1 F 8 10 18 0 8 F0 FD F2 D 212 21D 21
0 E
3nde;ed user plots can be used 'ith inde;ed -".T" se%uences and inde;ed G-- !iles 0see the section called &e3 ence and Annotation ,ile ,ormats in Chapter 11( The se%uence can then be changed using the drop do'n menu in the 8ntry toolbar and this 'ill change the graph data to the selected se%uence( F( the ne;t t'o !ormats are types o! 2iggle !ormats( The !irst is &ariable.tep( $ote that "rtemis only supports the colour element in the trac@ line(
track t&pe='iggle_0 color= 881 0010 (ariable5tep chrom=chr1D span=10 F10 1 F 0 1 FF0 1E F20 N F80 8 2F0 F 220 1
Right clic@ing on the graph and selecting the MCon!igure(((M option 'ill display the M,lot styleM option !or 'iggle plots( The plots can be displayed as histograms or as a heat map( ( the ne;t !ormat supported by "rtemis is !i;ed.tep and is again a 2iggle !ormat(
track t&pe='iggle_0 name="fixed5tep" description="fixed5tep format" (isibilit&=full auto5cale=off (ie'?imits=0#1000 color=01 001100 maxLeight@ixels=100#80# 0 graphT&pe=points priorit&= 0 fixed5tep chrom=chr1D start=G201 step=F00 span= 00 1000 D00 E00 G00 N00 800 200 F00 00 100
H( 9last tabular !ormat( The blastall command must be run 'ith the -m U !lag 'hich generates one line o! in!ormation per 4.,( "lternati&ely the 7.,crunch !ile !ormat can be read in as a graph !ile !ormat( "rtemis 'ill prompt the user to determine 'hether it uses the %uery or subGect coordinates to plot the graph(
2hen a !ile is prompted !or there is an option 'hich i! selected 'ill mean the log trans!orm is plotted(
!C Content IKJ
Controls 'hether the GC content plot is &isible( This is a graph o! the a&erage GC content o! a mo&ing 'indo' 0de!ault siIe 120 base1/ across the bases &isible in the o&er&ie' 'indo'( P#e!aultJ o!!Q Pshort nameJ gc_contentQ
A! Content IKJ
Controls 'hether the "G content plot is &isible( This is a graph o! the a&erage "G content o! a mo&ing 'indo' 0de!ault siIe 120 base1/ across the bases &isible in the o&er&ie' 'indo'( P#e!aultJ o!!Q Pshort nameJ ag_contentQ
!C .rame /lot
Controls 'hether the GC !rame plot is &isible( This graph is similar to the GC content graph but sho's the GC content o! the !irst/ second and third position independently( -or more in!ormation on the algorithm and on ho' to interpret the result see this 'eb page( .ee 3shi@a'a/ =( and 4otta/ A( -87. 7icrobiol( Lett( 1:FJ2 1-2 3 019991 and GC !rame plot !or more in!ormation on the algorithm( P#e!aultJ o!!Q Pshort nameJ gc_frameQ
Correlation Scores
Controls 'hether the 0!or'ard1 correlation scores plot is &isible( The graph sho's the correlation bet'een the amino acid composition o! the globular proteins in TR879L and the composition o! the base translation in each o! the three reading !rames( The green line represents !or'ard !rame 1/ blue represents !rame 2 and red represents !rame 3( P#e!aultJ o!!Q Pshort nameJ correlation_scoreQ
!C 8e$iation I!0CJ(I!;CJ
Controls 'hether the GC de&iation plot is &isible( This graph sho's the di!!erence bet'een the ?G? content o! the !or'ard strand and the re&erse strand( .ee ?"symmetric substitution patterns in the t'o #$" strands o! bacteria? Lobry =R( - 7ol 9iol 8&ol 199H 7ay)130 1JHH0- ( P#e!aultJ o!!Q Pshort nameJ gc_de(iationQ
AT 8e$iation IA0TJ(IA;TJ
Controls 'hether the "T de&iation plot is &isible( This graph sho's the di!!erence bet'een the ?"? content o! the !or'ard strand and the re&erse strand( P#e!aultJ o!!Q Pshort nameJ at_de(iationQ
Cumulati$e AT S5e- and Cumulati$e !C S5e"T s@e' is calculated as 0P"Q-PTQ1*0P"QEPTQ1/ 'here P"Q and PTQ are the counts o! these bases in the 'indo'( Grigorie& " 019991 .trand-speci!ic compositional asymmetries in double-stranded #$" &iruses( Cirus Research H0/ 1-19(
/ositional Asymmetry
.hulman 7=/ .teinberg C7/ 2estmoreland $ 019U11 The coding !unction o! nucleotide se%uences can be discerned by statistical analysis( = Theor 9iol UUJF09-20(
Informational 3ntropy
Aonop@a "ndrIeG 019UF1 3s the in!ormation content o! #$" e&olutionarily signi!icant< = Theor 9iol 10:JH9:-:0F( 3n!ormational entropy is calculated !rom a table o! o&erlapping #$" triplet !re%uencies/ using e%uation 1 in the abo&e re!erence( The use o! o&erlapping triplets smooths the !rame e!!ect(
Sho- 4ase HieThis toggle controls 'hether the base &ie' is &isible( 0see the section called +he O2er2ie( and DNA 0ie(s1( P#e!aultJ onQ
Chan"in" the Selection from a Hie- WindoTo select a !eature Gust clic@ on it 'ith the !irst mouse button( This 'ill unselect anything that is currently selected( To add a !eature to the selection rather than replacing the current selection/ hold the shift @ey
'hile clic@ing( " single !eature can be remo&ed !rom the selection in the same 'ay/ because shi!t-clic@ing acts as a toggle( The situation is made slightly more complicated by the e;istence o! spliced genes( 2hen a !eature segment 0e;on1 is added to the selection the !eature that contains the segment is implicitly added as 'ell( 2hen the last segment o! a !eature is remo&ed !rom the selection/ the !eature is implicitly remo&ed( " single base or amino acid can be selected simply by clic@ing on it( " range o! bases can be added by clic@ing on the base at one end o! the range then shi!t-clic@ on the base at the other end o! the range( "lternati&ely you can drag out a range o! basesJ clic@ on a base then hold the mouse button do'n and mo&e to the other end( To select a complete open reading !rame 05R-1/ double clic@ the middle mouse button 0see the section called Notes on !sing +he -o se1 any'here inside the 5R- 0see the section called Open Reading ,rame !or another 'ay to select an 5R-1( .ee the section called +he &election in Chapter 1 !or more about the selection(
'idth( Select Hisible Ran"e. .elect the currently &isible bases on the !or'ard strand( Select Hisible .eatures. .elect those 0and only those1 !eatures that currently &isible in this &ie'( "ny !eatures that are o!! screen or ha&e been !iltered out 'ith the ?.et .core Cuto!!s (((? control( Set Score Cutoffs ... The score cuto!!s panel allo's the user to !ilter the !eatures o! the acti&e entries so that !eatures 'ith lo' or high scores are not sho'n( The ?score? o! a !eature is the &alue o! the $score %uali!ier and should be a number !rom 0 to 100( The cuto!!s 'indo' has t'o sliders( "ny !eature that has a score less than the &alue o! the top controller or more than the &alue o! the bottom controller 'ill not be sho'n( -eatures 'ith no $score %uali!ier 'ill al'ays be sho'n(
To""le 4uttons
.eature Labels This toggle button controls 'hether the !eature labels are displayed on their o'n line 0'hen the toggle is on1 or on the top o! the !eatures 0'hen the toggle is o!!1( The de!ault setting !or this toggle can be set in the options !ile 0see the section called feature_labels in Chapter H1(
,ne Line /er 3ntry This toggle controls 'hether the entries are sho'n in the conte;t o! the three !rame translation or one entry per line on screen( 3n the !irst case the entries 'ill be o&erlaid/ in second case they 'ill be sho'n in parallel( The de!ault setting !or this toggle can be set in the options !ile 0see the section called one_line_per_entry in Chapter H1(
.or-ard .rame Lines This toggle button controls 'hether or not to sho' the 3 !rame translation o! the !or'ard se%uence(
Re$erse .rame Lines This toggle button controls 'hether or not to sho' the 3 !rame translation o! the re&erse se%uence(
Start Codons Toggle the display o! start codons in the &ie'( .ee the section called Genetic Code +ables in Chapter 2 to !ind out ho' to change 'hich start codons to use(
.eature Arro-s Toggle the display o! directional arro's on each !eature( The de!ault setting !or this toggle can be set in the options !ile 0see the section called draw_feature_arrows in Chapter H1(
.eature 4orders Toggle the display o! blac@ borders around each !eature( The de!ault setting !or this toggle can be set in the options !ile 0see the section called draw_feature_borders in Chapter H1(
All .eatures ,n .rame Lines $ormally non-protein !eatures are dra'n on the #$" lines( This toggle allo's the user to !orce all !eatures to be dra'n on the !rame lines/ 'hich can sometimes impro&e readability( The de!ault setting !or this toggle can be set in the options !ile 0see the section called features_on_frame_lines in Chapter H1(
.lip 8isplay 3! selected the se%uence and !eatures 'ill be dra'n on screen as i! they are re&erse complemented 'ith the !irst base to the right o! the screen(
Colourise 4ases This toggle turn base colouring on or o!!( 0$ote that this !eature is completely unless/ it e;ists !or amusement only1(
Scrollin" The Hie7o&ing the horiIontal scrollbar 'ill change the part o! the se%uence that is &isible( The position o! the &ie' can also be changed by using the Goto menu 0see the section called +he Goto -en 1/ by double clic@ing the !irst mouse button on a !eature in one o! the se%uence &ie's or in the !eature list or by double clic@ing on a base or amino acid(
28irect 3ditin"2
The direct editing option 0.ee the section called Enable Direct Editing in Chapter 21 enables the user to change the start or end position o! a segment by dragging it around 'ith the mouse( This 'or@s best in the #$" &ie' 'indo'( "s an e;ample/ to mo&e the start position/ clic@ the mouse button on the !irst base o! the !eature or e;on/ hold the button do'n/ mo&e the mouse pointer to the desired position/ then release the button(
themsel&es on that !eature( " double clic@ o! the middle mouse button on a !eature 'ill open an edit 'indo' !or that !eature( This is the same as clic@ing once and then choosing the 8dit .elected -eatures menu item 0see the section called &elected ,eat res in Editor 1(
Sho- 7ualifiers
3! this option is on the !eature %uali!iers 'ill be displayed a!ter the note(
Sho- /roduct
This button controls 'hether the $note or $product is sho'n !or each !eature( Pde!aultJ $note Q
Chapter @. /ro=ect .ile Mana"er ,$er$ieThe ,roGect -ile 7anager can be used to !acilitate the launching o! groups o! !iles together( The proGect details are stored bet'een sessions o! "rtemis/ so that it is straight!or'ard to return to a proGect and open
Chapter :. Secure Shell ISSGJ /lu"in To Artemis ,$er$ie- of the SSG /lu"in
This is a plug-in to "rtemis that enables you to &ie' and trans!er !iles !rom a local machine 0e(g( ,C*7ac5.>*+$3>1 to another remote !ile system 0i(e( any other !ile system that you ha&e ssh access to1( The main areas 'here this is use!ul areJ !ile management !or both local and remote !iles( -iles can be trans!erred by dragging and droping bet'een !ile systems( 7ultiple !iles can be selected and trans!erred in this 'ay( launching "rtemis and "CT 'ith se%uences and tab !iles !rom !iles on the remote machines( running 9L".T and -asta searches can be sent !rom the local machine that is running "rtemis and run on the remote machine( To do this the so!t'are 09L".T and -asta1 need to be set up on the remote side 0see the section called Config ring &earches to be r n 2ia &&91(
Lo"in In
-rom the "rtemis launch 'indo' go to the M-ileM menu and select M5pen ..4 -ile 7anagerM( " !ile manager 'indo' 'ill then open 'ith a local !ile manager at the top( +nderneath this is a remote !ile manager 'ith a section to enter login details(
3! you can connect directly to the remote machine gi&e the hostname/ username and pass'ord( "lternati&ely i! you are using a ..4 tunnel 0see the section called &etting p a &&9 t nnel1 then use localhost and the appropriate port number(
5n !NI" the ssh con!iguration can be set in the !ile *$+ssh$config( This contains the in!ormation to set up a tunnel that loo@s li@e thisJ
Lost U+sanger+ac+uk ?ocalFor'ard ;ser tMc machine+sanger+ac+uk#
5nce this con!iguration !ile is in place you can login !rom a +$3> 'indo' to set up a tunnel( 5n 'indo(s you can use ,utty/ see the section called !sing 1 tty to &et !p A + nnel( 2hen the tunnel has been established you can start artemis and enter MlocalhostM into the 4ostname !ield in the login 'indo' and the port number 0e(g( 2222 in the abo&e e;ample1(
The !ile manager can be used to drag and drop !iles bet'een each !ile system( 3! you right clic@ on a selected !ile this 'ill pro&ide you 'ith a pop-up menu 0see belo'1 enabling you to delete/ rename and open !iles(
-iles on the remote !ile system can be double clic@ed on and opened in "rtemis 0in the same 'ay they can be opened !rom the local !ile manager1( Tab !iles can be read in by dragging them !rom the remote !ile manager and dropping them into the "rtemis 'indo'( $ote !or "CT the se%uence !ilename can be dragged !rom the !ile manager into the !ile selection bo; 0i! the !iles are not !ound locally the are then located on the ser&er1( The tab !iles in "CT can be dragged !rom the !ile manager and dropped on the rele&ant se%uence display( 2hen !iles are sa&ed/ i! the entry orginated !rom the remote !ile system then this is sa&ed locally in the current 'or@ing directory and to the remote !ile as 'ell(
.et the source port to 2222 and set the destination to hostnameJport 0e(g( pcs2(internal(sanger(ac(u@J221(
Run "rtemis and select the M..4 -ile 7anagerM !rom the M-ileM menu( "t the bottom !ill in login details and clic@ on the MConnectM button( Loging in may ta@e a minute 0depending on the connection1(
Then trans!er this !ile to the local proGect directory and e;tract 'ithJ
tar x(f tar_ball_name+tar
'hen launching "rtemis/ ma@e sure you !irst change directory to the directory abo&e the M!astaM directory that has been unpac@ed( open the !iles !rom the remote !ile system in the !ile manager( 3t then @no's 'here to sa&e it bac@ to(
. . . remote directories to use as roots in the file manager remotedir+@D=$nfs$pathdata remotedir+I@=$nfs$disk $&eastpub . local directories to use as roots in the file manager localdir+@D=$nfs$pathdata localdir+I@=$nfs$disk $&eastpub
font_si)e
This option 'ill set the !ont siIe !or all the "rtemis 'indo's( Pde!aultJ 1FQ
font_name
This option is used to choose the !ont !or all the "rtemis 'indo's( The !ont must be !i;ed-'idth( Pde!aultJ ?7onospaced?Q
base_plot_height
The height 0in pi;els1 o! each o! the base plots( Pde!aultJ 1 0Q
feature_plot_height
The height 0in pi;els1 o! each o! the !eature plots( Pde!aultJ 1H0Q
dra'_feature_borders
3! set to yes/ borders 'ill be dra'n around each !eature and each e;on( i! set to no/ borders 'ill only be dra'n around the selected !eatures( This can also be set in the &ie's popup menu 0see the section called ,eat re Borders in Chapter 31( Pde!aultJ ?yes?Q
sho'_for'ard_lines
3! set to yes/ the !or'ard !rame lines are sho'n by de!ault( This can also be set in the &ie's popup menu( Pde!aultJ ?yes?Q
sho'_re(erse_lines
3! set to yes/ the re&erse !rame lines are sho'n by de!ault( This can also be set in the &ie's popup menu( Pde!aultJ ?yes?Q
dra'_feature_arro's
3! set to yes/ a direction arro' 'ill be dra'n around at the end o! each !eature( i! set to no/ no arro's 'ill be dra'n( This can also be set in the &ie's popup menu 0see the section called ,eat re Arro(s in Chapter 31( Pde!aultJ ?yes?Q
o(er(ie'_feature_labels
3! this option is no then the !eature labels in the o&er&ie' 0see the section called O2er2ie( of the Entry Edit 'indo( in Chapter 31 'ill be o!! at startup( Pde!aultJ ?yes?Q
o(er(ie'_one_line_per_entr&
3! this option is set yes then the o&er&ie' 0see the section called O2er2ie( of the Entry Edit 'indo( in Chapter 31 'ill start in one line per entry mode( Pde!aultJ ?no?Q
sho'_list
3! set to yes then the !eature list 0see the section called +he ,eat re $ist in Chapter 31 'ill be sho'n on startup( Pde!aultJ ?yes?Q
sho'_base_(ie'
3! set to yes then the #$" base &ie' 0see the section called +he O2er2ie( and DNA 0ie(s in Chapter 31 'ill be sho'n on startup( Pde!aultJ ?yes?Q
features_on_frame_lines
3! set to yes then the ?"ll -eatures 5n -rame Lines? option 'ill be set to yes on startup( 0.ee the section called All ,eat res On ,rame $ines in Chapter 31 Pde!aultJ ?no?Q
frame_line_features
This is a list o! the !eature @eys that should be sho'n by de!ault on the !rame lines( e(g(
frame_line_features = !D5 W pol&peptide W
feature_labels
3! set to yes then the !eature labels 'ill be sho'n on startup( 0.ee the section called All ,eat res On ,rame $ines in Chapter 31 Pde!aultJ ?yes?Q
one_line_per_entr&
3! set to yes then the ?5ne Line ,er 8ntry? option 'ill be set to yes on startup( 0.ee the section called All ,eat res On ,rame $ines in Chapter 31 Pde!aultJ ?no?Q
genetic_codes
This option gi&es the list o! names o! the a&ailable genetic code tables( -or each name in the list there is a translationKtableK$+798R entry 0see belo'1 'here $+798R is its location in the geneticKcodes list( .imilarly the start codons are de!ined as startKcodonsK$+798R !or each code(
translation_table_1
The translationKtable option is used to loo@up codon translations( The table must ha&e e;actly HF entries/ and there is one entry !or each codon( The entries should appear in this orderJ
TTT TT! TT> TT9 T!T T!! +++ +++
This is the de!ault setting !or this option is the .tandard CodeJ
translation_table_1 = W f f l l W s s s s W & & U U W c c U ' W W l l l l W p p p p W h h q q W r r r r W W i i i m W t t t t W n n k k W s s r r W W ( ( ( ( W a a a a W d d e e W g g g g
The other translation table entries are de!ined by gi&ing the di!!erences to the .tandard Code( These are gi&en as the bases that ma@e up the codon immediately !ollo'ed by the translation 0e(g( atam/ so that MataM codes !or MmM1(
extra_ke&s
This contains a list o! @eys 0separated by spaces1 that are allo'ed in addition to those speci!ied by 879L( The o!!icial 879L @eys are listed in the feature_ke&s !ile in the "rtemis code directory(
extra_qualifiers
This contains a list o! %uali!iers 0and their associated type1 that are allo'ed in addition to those speci!ied by 879L( The o!!icial 879L %uali!iers and %uali!ier types are listed and described in the qualifier_t&pes !ile in the "rtemis code directory(
common_ke&s
This is a list o! the @eys that should be sho'n by de!ault in the !eature edit 'indo'( 0see the section called &elected ,eat res in Editor in Chapter 31( The de!ault setting !or this option isJ
common_ke&s = W allele attenuator !D5 conflict exon intron ?T= misc_feature misc_=:> m=:> W mutation pol&>_signal pol&>_site promoter protein_bind =A5 repeat_region W repeat_unit r=:> sc=:> sn=:> source stem_loop 5T5 T>T>_signal terminator W t=:> unsure (ariation -10_signal -F8_signal !D5_motif gene W A?>5T:_L7T !D5_A<FK=< !D5_>FT<= A?>5T!D5
h&perlinks
This is a list o! databases and their +RLMs !or "rtemis to pro&ide hyperlin@s in the -eature 8ditor 0see the section called &elected ,eat res in Editor in Chapter 31(
undo_le(els
The number o! le&els o! undo to sa&e or 0 to disable undo( 7ore undo le&els 'ill re%uire more memory( Pde!aultJ 20Q
minimum_orf_si)e
This option is used to set the minimum siIe 0in amino acid residues1 o! a ?large? open reading !rame/ 'hich controls 'hich 5R-. are mar@ed by the ?7ar@ 5pen Reading -rames? menu item 0see the section called -ar) Open Reading ,rames ... in Chapter 31(
direct_edit
.et the de!ault &alue !or the direct edit option( " &alue o! ?yes? 'ill turn direct edit on by de!ault( .ee the section called Enable Direct Editing in Chapter 2
feature_dna_programs
This is a list o! the possible e;ternal programs that can be run on the bases o! a !eature( 8ach pair in the list is a program name and a de!ault database to use !or that program( -or each program name there must be a corresponding shell script called ?runKsomething?( eg( runKblastn( .ee the section called Config ring the R n -en in Chapter 3 !or more in!ormation(
feature_protein_programs
This is a list o! the possible e;ternal programs that can be run on the translation o! a !eature( 8ach pair in the list is a program name and a de!ault database to use !or that program( -or each program name there must be a corresponding shell script called ?runKsomething?( eg( runKblastp !or blastp or runK!asta !or !asta( .ee the section called Config ring the R n -en in Chapter 3 !or more in!ormation(
ncbi_dna_search
This lists the $C93 'eb-9L".T applications that the bases o! a selected !eature can be sent to( .ee the section called +he R n -en in Chapter 3(
ncbi_protein_search
This lists the $C93 'eb-9L".T applications that the translation o! a selected !eature can be sent to( .ee the section called +he R n -en in Chapter 3(
Settin" Colours
The !eature colours 0see the section called ,eat re Colo rs in Chapter 11 used by "rtemis can be changed using the options !ile( 9y de!ault there are 1U possible colours 0numbered 0 to 1:1/ but any number can be used( The option names !or the colours are colour_0/ colour_1/ etc( The &alue o! each o! these %uali!iers should be the three numbers separated by spaces( The numbers correspond to red/ green and blue respecti&ely and each number is an intensity !rom 0 to 2 ( "s an e;ample/ to change colour 2 to 'hite put this line in the options !ileJ
colour_
88
88
88
Pde!aultJ ?e;on-model?Q
chado_transcript
This is the !eature @ey used 'hen chado transcripts are created in a gene model( Pde!aultJ ?mR$"?Q
chado_ser(ers
This can be used to pro&ide a list o! a&ailable databases( -or e;ampleJ
chado_ser(ers = W test localhost#82F $test%user:ame W genedb_ro db+genedb+org#82F $snapshot%genedb_ro
3! the &alue o! an options is too long to !it on one line it can be split o&er se&eral lines by ending each line 'ith a bac@slash li@e thisJ
option_name = option_(alue another_option_(alue W a_third_option_(alue a_forth_option_(alue