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BMCBI
2010

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model

9 years 4 days ago
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
Background: While most multiple sequence alignment programs expect that all or most of their input is known to be homologous, and penalise insertions and deletions, this is not a reasonable assumption for non-coding DNA, which is much less strongly conserved than protein-coding genes. Arguing that the goal of sequence alignment should be the detection of homology and not similarity, we incorporate an evolutionary model into a previously published multiple sequence alignment program for non-coding DNA, Sigma, as a sensitive likelihood-based way to assess the significance of alignments. Version 1 of Sigma was successful in eliminating spurious alignments but exhibited relatively poor sensitivity on synthetic data. Sigma 1 used a p-value (the probability under the "null hypothesis" of non-homology) to assess the significance of alignments, and, optionally, a background model that captured short-range genomic correlations. Sigma version 2, described here, retains these features,...
Gayathri Jayaraman, Rahul Siddharthan
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Gayathri Jayaraman, Rahul Siddharthan
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