A sensitive short read homology search tool for paired-end read sequencing data.

ABSTRACT:

Background

Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq da

SUBMITTER: Techa-Angkoon P 

PROVIDER: S-EPMC5657049 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature