Functional annotation V1.2

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Functional annotation of the Physcomitrella patens protein coding genes V1.2

Existing functional annotation like gene names, description lines, GO terms and Kegg EC numbers and KO term was collected from several resources and combined into non-redundant database.

Additional functional annotation was created using the homology-based methods BLAST2GO, IPRScan and KAAS. These two steps resulted in GO terms with IEA evidence codes.

Subcellular localization of the protein sequences was predicted under consideration of the individual gene's full-length status using several tools: MultiLoc,WolfPSORT, Targetp, Chlorop,SignalP, Prosite KDEL, HMMTOP and MEMSAT3.

To combine these predictions with the existing GOA, we developed the algorithm pred2GOA. Resulting predictions were translated into cellular component GO terms and compared to the existing GOA at the GO slim (plants) level.

In order to assign a GO term for a subcellular location, a least two predictors had to agree. If the underlying gene didn't have an annotated UTR and a start codon, at least one of the predictors predictions had to be based on more than the N-terminal region of the of the protein. Resulting GO terms were defined as ISS.

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