The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Domain enhanced lookup time accelerated BLAST
Open accessAbstract
BACKGROUND: BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM) for searching the database in round i + 1. Biegert and Söding developed Context-sensitive BLAST (CS-BLAST), which combines information from searching the sequence database with information derived from a library of short protein profiles to achieve better homology detection than PSI-BLAST, which builds its PSSMs from scratch. RESULTS: We describe a new method, called domain enhanced lookup time accelerated BLAST (DELTA-BLAST), which searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI's Conserved Domain Database (CDD). On a test set derived from ASTRAL, with one round of searching, DELTA-BLAST achieves a ROC5000 of 0.270 vs. 0.116 for CS-BLAST. The performance advantage diminishes in iterated searches, but DELTA-BLAST continues to achieve better ROC scores than CS-BLAST. CONCLUSIONS: DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the "Protein BLAST" link at http://blast.ncbi.nlm.nih.gov.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Self-citationGapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
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Cited by
BLAST: a more efficient report with usability improvements
Boratyn, G. M., Camacho, C., Cooper, P. S., Coulouris, G., Fong, A., Ma, N., Madden, T. L., Matten, W. T., McGinnis, S. D., Merezhuk, Y., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt282 · Cited by 1,369
Self-citationLu, K., Psakhye, I., & Jentsch, S. (2014) · Cell · doi:10.1016/j.cell.2014.05.048 · Cited by 346
Luo, Q., Kumar, P., Vickers, T. J., Sheikh, A., Lewis, W. G., Rasko, D. A., Sistrunk, J., & Fleckenstein, J. M. (2014) · Infection and Immunity · doi:10.1128/iai.01106-13 · Cited by 139
Cicconardi, F., Milanetti, E., Pinheiro de Castro, E. C., Mazo-Vargas, A., Van Belleghem, S. M., Ruggieri, A. A., Rastas, P., Hanly, J., Evans, E., Jiggins, C. D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41412-5 · Cited by 81
A CPF-like phosphatase module links transcription termination to chromatin silencing
Mateo-Bonmatí, E., Montez, M., Maple, R., Fiedler, M., Fang, X., Saalbach, G., Passmore, L. A., & Dean, C. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.05.016 · Cited by 30
Metadata
- Authors
- Boratyn, G. M., Schäffer, A. A., Agarwala, R., Altschul, S. F., Lipman, D. J., & Madden, T. L.
- Venue
- Biology Direct
- Published
- 2012
- Volume
- 7
- Issue
- 1
- Pages
- 12
- ISSN
- 1745-6150 (ISSN-L)
- OpenAlex
- W2163910672
- Cited by
- 799
- References
- 2
- FWCI
- 15.45
- Type
- journal article
- Language
- en
- Open access
- gold
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