Abstract
BackgroundThe 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.ResultsWe 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. The tool in particular tackles the problem of identifying those coding exon groups that belong to the same paralogous genes in a fragmented genome assembly. This paralog-to-contig assignment problem is shown to be NP-complete. It is phrased and solved as an Integer Linear Programming problem.ConclusionsThe ExonMatchSolver-pipeline can be employed to build highly accurate models of protein coding genes even when spanning several genomic fragments. This sets the stage for a better understanding of the evolutionary history within particular gene families which possess a large number of paralogs and in which frequent gene duplication events occurred.Electronic supplementary materialThe online version of this article (doi:10.1186/s13015-016-0063-y) contains supplementary material, which is available to authorized users.
Highlights
The accurate annotation of genes in newly sequenced genomes remains a challenge
If the contigs in Pipeline overview The conceptual translation of the coding portion of an individual exon, a translated coding exon (TCE) for short, is treated as elementary building block
The ExonMatchSolver-pipeline (EMS-pipeline) implements a work-flow comprising four main steps: (1) the search of protein sequences or protein-models specific for paralogs and individual TCEs against a complete target genome, (2) the paralog-tocontig assignment formulated as an Integer Linear Programming (ILP) problem, (3) a refined search for exons missing after step 2 relative to the input gene models, and (4) the assembly of fragmented hits and the proposition of gene annotations
Summary
Sophisticated comparative pipelines are available, computationally derived gene models are often less than perfect This is true when multiple similar paralogs are present. Accurate multiple sequence alignments are required as input for a wide variety of different computational analysis techniques in phylogenetics, molecular evolution and comparative genomics. In this contribution we will primarily be concerned with protein coding regions. Many large protein families, such as transcription factors, growth factors, proteins involved in signaling pathways and membrane proteins, include paralogous members that share highly similar sequence elements. One key issue, which is the main motivation for this contribution, is the availability and quality of the input sequence data
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