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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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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