Domain enhanced lookup time accelerated BLAST
By G. Boratyn, Alejandro A. Schäffer, Richa Agarwala, Stephen F. Altschul, David J. Lipman, Thomas L. Madden. Biology Direct, 2012
793 citations recorded by the source corpus.
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. 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. 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. This article was reviewed by Arcady Mushegian, Nick V. Grishin, and Frank Eisenhaber.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/6bc7471f5e3e121dbe05d2caa170a4209c1e8380
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Thomas L. Madden
- Christoph Peters
- Scott D. McGinnis
- Jian Ye
- Yan Raytselis
- Ning Ma
- George F. Coulouris
- Christiam Camacho
In Spectroscopy
Citations in the corpus
- Topology Prediction of α-Helical Transmembrane Proteins (2016, methodology): “Further developments of BLAST are Position-Specific Iterative BLAST (PSI-BLAST) [57] and domain enhanced lookup time accelerated BLAST (DELTA-BLAST) [58].”
- The BLAST Sequence Analysis Tool (2013, background): “Third, Splitd pulls the search from the SQL database [4], queues it, and spreads it across several backends [5].”
- BLAST: a more efficient report with usability improvements (2013, methodology): “Finally, BLAST offers sensitive protein–protein searches using PSI-BLAST (1,7) and DELTA-BLAST (8).”