Predicting the functional repertoire of an organism from unassembled RNA-seq data.

ABSTRACT:

Background

The annotation of biomolecular functions is an essential step in the analysis of newly sequenced organisms. Usually, the functions are inferred from predicted genes on the genome using homology search techniques. A high quality genomic sequence is an important prerequisite which, however, is difficult to achieve for certain organisms, such as hybrids or organisms with a large genome. For functional analysis it is also possible to use a de novo transcriptome assembly but the computational requirements can be demanding. Up to now, it is unclear how much of the functional repertoire of an organism can be reliably predicted from unassembled RNA-seq short reads alone.

Results

We have conducted a study to investigate to what degree it is possible to reconstruct the func

SUBMITTER: Landesfeind M 

PROVIDER: S-EPMC4258056 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature