Title |
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
|
---|---|
Published in |
Nucleic Acids Research, September 1997
|
DOI | 10.1093/nar/25.17.3389 |
Pubmed ID | |
Authors |
Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, David J. Lipman |
Abstract |
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 2 | 11% |
Saudi Arabia | 2 | 11% |
Colombia | 1 | 6% |
Switzerland | 1 | 6% |
Denmark | 1 | 6% |
New Zealand | 1 | 6% |
Unknown | 10 | 56% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 9 | 50% |
Scientists | 8 | 44% |
Science communicators (journalists, bloggers, editors) | 1 | 6% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 183 | 1% |
United Kingdom | 82 | <1% |
Germany | 81 | <1% |
Brazil | 64 | <1% |
Spain | 38 | <1% |
France | 30 | <1% |
Canada | 28 | <1% |
Mexico | 27 | <1% |
India | 23 | <1% |
Other | 301 | 2% |
Unknown | 13294 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 3180 | 22% |
Researcher | 2289 | 16% |
Student > Master | 1986 | 14% |
Student > Bachelor | 1739 | 12% |
Student > Doctoral Student | 709 | 5% |
Other | 2116 | 15% |
Unknown | 2132 | 15% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 5812 | 41% |
Biochemistry, Genetics and Molecular Biology | 2782 | 20% |
Computer Science | 636 | 4% |
Chemistry | 453 | 3% |
Immunology and Microbiology | 372 | 3% |
Other | 1594 | 11% |
Unknown | 2502 | 18% |