David Lutz

CARTOONING

CARTOONING_116_PROPOSAL
In bioinformatics , the full general lineament format ( gene-finding format , generic feature
formatting , GFF ) is a data file format used for describing factor and early features of DNA ,
ribonucleic acid and protein succession .== GFF variant == The follow versions of GFF exist :
universal feature film Format Version 2 , generally deprecated cistron transport Format
2.2 , a first derivative used by Ensembl Generic Feature Format Version 3 Genome variance
formatting , with additional pragmas and attributes for sequence alteration
featuresGFF2/GTF had a number of deficiencies , notably that it can only represent two-
level feature hierarchies and thus can not handle the three-level hierarchy of gene →
transcript → exon .GFF3 addresses this and other deficiencies .For example , it supports
arbitrarily many hierarchal floor , and gives specific signification to sealed tag end in the
attribute sphere .The GTF is identical to GFF , version 2 .== GFF full general structure == All
GFF formats ( GFF2 , GFF3 and GTF ) are tab delimited with 9 fields per occupation .They all
share the Saame structure for the first 7 theatre of operations , while differing in the content
and format of the 9th field .Some landing field figure have been changed in GFF3 to stave off
confusedness .For good example , the `` seqid '' field was formerly referred to as `` sequence
'' , which may cost confused with a base or amino acid mountain range .The ecumenical
structure is as follows : === The 8th field : phase of Cd characteristic === Simply put ,
candela means `` CoDing succession '' .The exact meaning of the term is defined by sequence
Ontology ( so ) .According to the GFF3 specification : For features of type `` atomic number
48 '' , the phase indicates where the feature begins with character to the meter reading
human body .The stage is one of the whole number 0 , 1 , or 2 , indicating the identification
number of bases that should be removed from the beginning of this feature to reach the
start base of the future codon .=== Meta Directives === In GFF files , additional meta data
can live included and follows after the # # directive .This meta information can detail GFF
version , sequence neighborhood , or mintage ( full tilt of meta information character can
represent found at Sequence Ontology specification ) .== GFF software == === server ===
Servers that generate this data formatting : === Clients === client that use this data format :
=== Validation === The modENCODE project hosts an online GFF3 validation tool with
generous limits of 286.10 MB and 15 million production line .The Genome Tools software
program collection contains a gff3validator tool that can follow used offline to validate and
possibly straighten GFF3 filing cabinet .An online proof service is also usable .