The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies.

ABSTRACT:

Background

The accurate annotation of genes in newly sequenced genomes remains a challenge. Although sophisticated comparative pipelines are available, computationally derived gene models are often less than perfect. This is particularly true when multiple similar paralogs are present. The issue is aggravated further when genomes are assembled only at a preliminary draft level to contigs or short scaffolds. However, these genomes deliver valuable information for studying gene families. High accuracy models of protein coding genes are needed in particular for phylogenetics and for the analysis of gene family histories.

Results

We present a pipeline, ExonMatchSolver, that is designed to help the user to produce and curate high quality models of the protein-coding part of genes

SUBMITTER: Indrischek H 

PROVIDER: S-EPMC4765045 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature