APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

MOTIVATION: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. RESULTS: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.


Publié dans:
Bioinformatics, 19 Suppl 1, i215-21
Année
2003
Note:
Department of Biochemistry, University College, Cork, Ireland.
Laboratoires:




 Notice créée le 2007-12-17, modifiée le 2018-12-03


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