APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
| Title | APDB: a novel measure for benchmarking sequence alignment methods without reference alignments |
| Publication Type | Journal Article |
| Year of Publication | 2003 |
| Authors | O'Sullivan, O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C |
| Journal | Bioinformatics |
| Volume | 19 Suppl 1 |
| Pagination | i215-21 |
| Accession Number | 12855461 |
| Keywords | Algorithms Amino Acid Sequence Benchmarking/ methods Molecular Sequence Data Reference Standards Reproducibility of Results Sensitivity and Specificity Sequence Alignment/ methods/standards Sequence Analysis, DNA/ methods/standards Sequence Analysis, Protein/ methods/standards Sequence Homology Software Software Validation |
| 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. |
- Research keywords:
- Software Validation,
- Software,
- Sequence Homology,
- Sequence Analysis, Protein/ methods/standards,
- Sequence Analysis, DNA/ methods/standards,
- Sequence Alignment/ methods/standards,
- Sensitivity and Specificity,
- Reproducibility of Results,
- Reference Standards,
- Molecular Sequence Data,
- Benchmarking/ methods,
- Amino Acid Sequence,
- Algorithms
