Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.

ABSTRACT:

Background

For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available.

Results

We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated pot

SUBMITTER: Amar D 

PROVIDER: S-EPMC4274702 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature