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Bioinformatics Advance Access published online on August 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth493
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 13, 2004
Revised August 18, 2004
Accepted August 19, 2004

Applications note

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

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

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

* To whom correspondence should be addressed. E-mail: ivwalle{at}vub.ac.be.


  Abstract

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 resp. very low and low to intermediate similarity. 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.


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