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This article is part of the supplement: Articles selected from posters presented at the Tenth Annual International Conference on Research in Computational Biology

Open Access Open Badges Research

Automatic extraction of reliable regions from multiple sequence alignments

Timo Lassmann1* and Erik LL Sonnhammer12

Author Affiliations

1 Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden

2 Stockholm Bioinformatics Center, Stockholm University, S-106 91 Stockholm, Sweden

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BMC Bioinformatics 2007, 8(Suppl 5):S9  doi:10.1186/1471-2105-8-S5-S9

Published: 24 May 2007



High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets while the accuracy of individual alignments is often overlooked.


We have previously developed a method to automatically assess the accuracy and overall difficulty of multiple alignments. This was achieved by a per-residue comparison between alternate alignments of the same sequences. Here we present a key extension to this method, an algorithm to extract similarly aligned regions from several alignments and merge them into a new consensus alignment.


We demonstrate that the fraction of correctly aligned residues within the resulting alignments is increased by 25 – 100 percent compared to the original input alignments, as only the most reliably aligned parts are considered.