Cosmoss Gene IDs

From PhyscomeProjectWiki

Revision as of 12:17, 20 December 2011 by Lang (Talk | contribs)
(diff) ←Older revision | Current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

Cosmoss locus and gene identifiers (CGI)

On cosmoss each gene model has an additional unique gene (locus) ID (CGI). The CGI provides a unique address to a gene (model). Using a clustering procedure, all overlapping gene models were grouped into a unique locus. For each locus a unique number was assigned, which is specific for a given assembly. All CGIs include the number of the scaffold and the number of the locus they belong as well as information on the version of the assembly and annotation or the gene predictor they are derived from.

CGI Syntax

They include information on:

  • the assembly version
  • the number of the scaffold
  • the number of the locus
  • the class: the version of the annotation release or the gene predictor that predicted the model
  • the splice variant

OrganismCode+AssemblyVersion+ScaffoldNumber+_+LocusNumber+Type+. + SpliceVariant

Pp1s275_3V2.1 (= Phypa_196781)


Type field

The type field indicates either the version of a released model (e.g. V1.2 or V1.5) or the predictor of a gene model in the all_models catalog.

Source Type Description
JGI_FM1 V0 V1.0
JGI_FM3 V1 V1.1
JGI_cosmoss V2 V1.2
JGI_e_gw1 G3
JGI_estExt_fgenesh1_kg F2
JGI_estExt_fgenesh1_pg F4
JGI_estExt_fgenesh1_pm F5
JGI_estExt_fgenesh2_kg F7
JGI_estExt_fgenesh2_pg F9
JGI_estExt_fgenesh2_pm F10
JGI_estExt_Genewise1 G2
JGI_estExt_gwp_gw1 G4
JGI_fgenesh1_kg F1
JGI_fgenesh1_pg F3
JGI_fgenesh2_kg F6
JGI_fgenesh2_pg F8
JGI_gw1 G1
JGI_user U1 User models
EuGene_newIMM E1
EuGene_newIMM3 E2
EuGene_newIMM3_trim_UTR E3
EVM_gth E4
Personal tools