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ALMOB
2006

Multiple sequence alignment with user-defined anchor points

9 years 1 months ago
Multiple sequence alignment with user-defined anchor points
Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our progr...
Burkhard Morgenstern, Sonja J. Prohaska, Dirk P&ou
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where ALMOB
Authors Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler
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