SABmark—a benchmark for sequence alignment that covers the entire known fold space
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Open Access
- 27 August 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 21 (7) , 1267-1268
- https://doi.org/10.1093/bioinformatics/bth493
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 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@vub.ac.beKeywords
This publication has 9 references indexed in Scilit:
- Align-m—a new algorithm for multiple alignment of highly divergent sequencesBioinformatics, 2004
- The ASTRAL Compendium in 2004Nucleic Acids Research, 2004
- OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracyBMC Bioinformatics, 2003
- BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutationsNucleic Acids Research, 2001
- Large-scale comparison of protein sequence alignment algorithms with structure alignmentsProteins-Structure Function and Bioinformatics, 2000
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal pathProtein Engineering, Design and Selection, 1998
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteinsProtein Engineering, Design and Selection, 1995
- SCOP: a structural classification of proteins database for the investigation of sequences and structures.Journal of Molecular Biology, 1995