Struktur motif protein dari gen-gen resisten

NBS-LRR

(Sumber: McHale, et al., 2006)

 Tersedia data sekuen yang mirip dengan gen
target
Tabel Klasifikasi beberapa gen resisten dari tumbuhan*)
Motif Struktur
Klas Gen Tumbuhan Patogen Referensi
protein R
Detoxifying
1 Hm1 Jagung Helmintosporium maydis enzyme, HC- Briggs (1992)
toxin reductase
Intracellular
Pseudomonas syringae Martin et al.
2 Pto Tomat ser/thr protein
(avrPto) 1993
kinase
Pseudomonas syringae
RPS2 RPM1 Arabidopsis- CC/NBS/LRR Bent et al. 1994
(avrRpt2)
3a
Pseudomonas syringae Grant et al.
Arabidopsis-
(avrRpm1/avrB) 1995

N Tembakau Tobacco mosaic virus TIR/NBS/LRR

Whitham et al.
3b L6 Flax Melampsora lini
1994
RPP5 Arabidopsis Peronospora parasitica
Jones et al.
Cf-2 Tomat Cladosporium fulvum
1994,
Dixon et al.
Cf-4 Extracellular
4 1996,
LRR
Dixon et al.
Cf-5
1998
Cf-9
Xa21 Rice Xanthomonas oryzae Extracellular Song et al. 1995
5 LRR/kinase
domain
 Tabel lambang nukleotid yang digunakan dalam penyusunan sekuen primer menurut
IUPAC (IUPAC-IUB. 1970; Cornish-Bowden. 1985).

Lambang Basa/nukleotid Lambang Basa Nukleotid

A Adenosine W A T (Weak interaction)
G T C (not A) (B comes
C Cytosine B
after A)
G A T (not C) (D comes
G Guanine D
after C)
A C T (not G) (H comes
T Thymidine H
after G)
G C A (not T, not U) (V
U Uracil V
comes after U)
R G A (puRine) N A G C T (aNy)
Y T C (pYrimidine) W A T (Weak interaction)
K G T (Ketone) X masked
gap of indeterminate
M A C (aMino group) -
length
G C (Strong
S
interaction)
Pendisainan Primer Degeneratif dari Data
Sekuens DNA

Jamsari, 2010
Pendisainan Primer Degeneratif dari Data
Sekuen asam amino
 Beberapa software untuk mendisain primer berbasis web (Abd-Elsalam, 2003)

Tool name Description www

CODEHOP Consensus Degenerate Hybrid Oligonucleotide Primers; http://blocks.fhcrc.org/codehop.html
degenerate PCR primer design; will accept unaligned
sequences.
Gene Fisher Interactive primer design tool for standard or degenerate http://bibiserv.techfak.uni-bielefeld.de/genefisher/
primers; will accept unaligned sequences.
DoPrimer Easily design primers for PCR and DNA sequencing. http://doprimer.interactiva.de/
Primer3 Comprehensive PCR primer and hybridization probe design http://www-genome.wi.mit.edu/cgi-
tool; many options but easy to accept defaults at first. bin/primer/primer3_www.cgi
http://www.basic.nwu.edu/biotools/Primer3.html
http://www.justbio.com/primer/index.php
Primer Selection Select PCR primers from nucleotide sequence. http://alces.med.umn.edu/rawprimer.html
Web Primer Allow alternative design of primers for either PCR or http://genome-www2.stanford.edu/cgi-
sequencing purpose. bin/SGD/web-primer
PCR Designer For restriction analysis of sequence mutations. http://cedar.genetics.soton.ac.uk/public_html/primer
.html
Primo Pro 3.4 Reduces PCR noise by lowering the probability of random http://www.changbioscience.com/primo/primo.html
primering.
Primo Degenerate 3.4 Primo Degenerate 3.4 designs PCR primers based on a single http://www.changbioscience.com/primo/primod.htm
peptide sequence or multiple alignments of proteins or l
nucleotides.
PCR Primer Design An application that designs primers for PCR or sequencing http://pga.mgh.harvard.edu/servlet/org.mgh.proteom
purposes. e.Primer
The Primer Generator The program analyzes the original nucleotide sequence and http://www.med.jhu.edu/medcenter/primer/primer.c
desired amino acid sequence and designs a primer that either gi
has a new restriction enzyme site or is missing an old one.
EPRIMER3 Picks PCR primers and hybridization oligos (EMBOSS). http://bioweb.pasteur.fr/seqanal/interfaces/eprimer3.
html
 Beberapa software untuk mendisain primer berbasis web (Abd-Elsalam, 2003)

PRIMO Prediction of forward and reverse oligonucleotide Primers.http://bioweb.pasteur.fr/seqanal/interfaces/primo.htm

l3
http://atlas.swmed.edu/primo/primo_form.html
PrimerQuest A primer design tool. http://www.idtdna.com/biotools/primer_quest/primer
_quest.asp
MethPrimer Design primers for methylation PCRs. http://itsa.ucsf.edu/~urolab/methprimer/index1.html
Rawprimer A tool for selection of PCR primers. http://alces.med.umn.edu/rawprimer.html
MEDUSA A tool for automatic selection and visual assessment of PCR http://www.cgr.ki.se/cgr/MEDUSA/
primer pairs.
The Primer Prim'er Software suite that completely automates the PCR primer http://www-
Project design process. nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer
_
Project/Primer.html
Oligonucleotides for Seek oligonucleotides on both sides of an area. http://www.citi2.fr/bio2/Oligo2lib.html
the PCR
GAP Genome- wide Automated Primer finder servers. http://promoter.ics.uci.edu/Primers/
 Beberapa software untuk pendisainan primer yang dapat didownload untuk
dioperasionalkan menggunakan personal computer. (Abd-Elsalam, 2003)

Software name Description www

PrimerSelect Analyzes a template DNA sequence and chooses primer pairs for PCR and primers for www.dnastar.com
DNA sequencing.
DNASIS Max DNASIS Max is a fully integrated program that includes a wide range of standard http://www.medprobe.com/no/dnasis.html
sequence analysis features.
Primer Premier 5 primer design for Windows and Power Macintosh. http://www.premierbiosoft.com/primerdesign/primerd
esign.html
Primer Premier: Comprehensive primer design for Windows and Power Macintosh. http://www.premierbiosoft.com/
NetPrimer Comprehensive analysis of individual primers and primer pairs. http://www.premierbiosoft.com/NetPrimer.html
Array Designer 2 For fast, effective design of specific oligos or PCR primer pairs for microarrays http://www.premierbiosoft.com/dnamicroarray/dnami
croarray.html
Beacon Designer Design molecular beacons and TaqMan probes for robust amplification and fluorescence http://www.premierbiosoft.com/molecular_beacons/ta
2.1 in real time PCR. qman_molecular_beacons.html
GenomePRIDE Primer design for DNA-arrays/chips. http://pride.molgen.mpg.de/genomepride.html
1.0
Fast PCR Software for Microsoft Windows has specific, ready-to-use templates for many PCR and http://www.biocenter.helsinki.fi/bi/bare-
sequencing applications: standard and long PCR, inverse PCR, degenerate PCR directly 1_html/manual.htm
on amino acid sequence, multiplex PCR.
OLIGO 6 Primer Analysis Software for Mac and Windows. http://www.oligo.net/
Primer Designer 4 Will find optimal primers in target regions of DNA or protein molecules, amplify features http://www.scied.com/ses_pd5.htm
in a molecule, or create products of a specified length.
GPRIME Software for primer design. http://life.anu.edu.au/molecular/software/gprime.htm
Sarani Gold Genome Oligo Designer is software for automatic large-scale design of optimal http://mail.strandgenomics.com/products/sarani/
oligonucleotide probes for microarray experiments.
PCR Help Primer and template design and analysis http://www.techne.com/CatMol/pcrhelp.htm
Genorama chip Genorama Chip Design Software is complete set of programs required for genotyping http://www.asperbio.com/Chip_desin_soft.htm
Design Software chip design. The programs can also be bought separately.
Primer Designer The Primer Designer features a powerful, yet extremely simple, real-time interface to http://genamics.com/expression/primer.htm
allow the rapid identification of theoretical ideal primers for your PCR reactions.
Primer Premier Automatic design tools for PCR, sequencing or hybridization probes, degenerate primer http://www.biotechniques.com/freesamples/itembtn21.
design, Nested/Multiplex primer design, restriction enzyme analysis and more. html
PrimerDesign DOS-program to choose primer for PCR or oligonucleotide probes. http://www.chemie.unimarburg.de/%7Ebecker/pdhom
e.html
Skema teknik inverse-PCR (iPCR) untuk mengidentifikasi sekuen pengapit
daerah yang sudah diketahui. (Sumber: Hui, et al., 1998)
Primer/Chromosome walking
Ekstensi Sekuens