Name
Abstract | ||
|---|---|---|
Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains-homologous over-extension (HOE). PSI-Search combines an optimal Smith-Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has similar to 4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2- for 4-fold fewer false-positives than JackHMMER, but is similar to 5% less sensitive. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1093/bioinformatics/bts240 | BIOINFORMATICS |
Keywords | Field | DocType |
sequence alignment,internet,computational biology,programming languages | Sequence alignment,Data mining,Computer science,Amino Acid Motifs,SOAP,Smith–Waterman algorithm,Bioinformatics,Web service,User interface,Perl | Journal |
Volume | Issue | ISSN |
28 | 12 | 1367-4803 |
Citations | PageRank | References |
8 | 0.66 | 10 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Weizhong Li | 1 | 239 | 19.23 |
| Hamish McWilliam | 2 | 855 | 88.74 |
| Mickael Goujon | 3 | 98 | 12.87 |
| Andrew Peter Cowley | 4 | 52 | 2.69 |
| Rodrigo Lopez | 5 | 4865 | 744.83 |
| William R Pearson | 6 | 26 | 1.66 |