Primary orthologs from local sequence context
نویسندگان
چکیده
منابع مشابه
Orthologs from maxmer sequence context
Context-dependent identification of orthologs customarily relies on conserved gene order or whole-genome sequence alignment. It is shown here that short-range context—as short as single maximal matches—also provides an effective means to identify orthologs within whole genomes. On pristine (un-repeatmasked) mammalian whole-genome assemblies we perform a genome “intersection” that in general con...
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Broadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) identify gene anchors and (iii) link anchors to identify best gene matches given their order and context. In this article, we engineer two methods to improve two important aspects of this pipeline [specifically steps (ii) and (iii)]. First, computing s...
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MOTIVATION Traditional bioinformatics methods scan primary sequences for local patterns. It is important to assess how accurate local primary sequence methods can be. RESULTS We study the problem of donor pre-mRNA splice site recognition, where the sequence overlaps between real and decoy datasets can be quantified, exposing the intrinsic limitations of the performance of local primary sequen...
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Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged after a speciation) is crucial and lies at the heart of many genomic studies. However, existing methods that rely only on 1:1 orthologs to infer species trees...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2020
ISSN: 1471-2105
DOI: 10.1186/s12859-020-3384-2