ArticleAlgorithms for molecular biology : AMB2016
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies.
Article in Algorithms for molecular biology : AMB, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Article
- ExceS-A: an exon-centric split aligner.Journal of integrative bioinformatics · 2022Article
- Draft genome of a biparental beetle species, Lethrus apterus.BMC genomics · 2021Article
- Article
- Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa.BMC evolutionary biology · 2018Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
- Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes.BMC evolutionary biology · 2017Article
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Authors and funding
4 authors.
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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.
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