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

Orla O'Sullivan; Mark Zehnder; Des Higgins; Philipp Bucher; Aurelien Grosdidier; Cédric Notredame

doi:10.1093/bioinformatics/btg1029

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

Orla O'Sullivan·Mark Zehnder·Des Higgins·Philipp Bucher·Aurelien Grosdidier·Cédric Notredame

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Abstract

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.

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Algorithms Amino Acid Sequence Benchmarking Molecular Sequence Data Reference Standards Reproducibility of Results Sensitivity and Specificity Sequence Alignment Sequence Analysis, DNA Sequence Analysis, Protein Sequence Homology Software Software Validation Comparative Study Evaluation Study Journal Article Validation Study

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BibTeX RIS

Orla O'Sullivan, Mark Zehnder, Des Higgins, Philipp Bucher, Aurelien Grosdidier, Cédric Notredame. 2003. APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.. https://doi.org/10.1093/bioinformatics%2Fbtg1029

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