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Bioinformatics Advance Access originally published online on August 27, 2004
Bioinformatics 2005 21(7):1267-1268; doi:10.1093/bioinformatics/bth493
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

SABmark—a benchmark for sequence alignment that covers the entire known fold space

Ivo Van Walle 1,*, Ignace Lasters 2 and Lode Wyns 1

1Department of Ultrastructure, Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussel, Belgium
2Algonomics NV Technologiepark 4, 9052 Gent-Zwijnaarde, Belgium

*To whom correspondence should be addressed.

Summary: The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem.

Availability: SABmark is available from http://bioinformatics.vub.ac.be

Contact: ivwalle{at}vub.ac.be


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