MOTIVATION: Many studies have shown that database searches using position-specific score matrices (PSSMs) or profiles as queries are more effective at identifying distant protein relationships than are searches that use simple sequences as queries. One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST). RESULTS: This paper describes a new software package, IMPALA, designed for the complementary procedure of comparing a single query sequence with a database of PSI-BLAST-generated PSSMs. We illustrate the use of IMPALA to search a database of PSSMs for protein folds, and one for protein domains involved in signal transduction. IMPALA's sensitivity to distant biological relationships is very similar to that of PSI-BLAST. However, IMPALA employs a more refined analysis of statistical significance and, unlike PSI-BLAST, guarantees the output of the optimal local alignment by using the rigorous Smith-Waterman algorithm. Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database.
MOTIVATION: Many studies have shown that database searches using position-specific score matrices (PSSMs) or profiles as queries are more effective at identifying distant protein relationships than are searches that use simple sequences as queries. One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST). RESULTS: This paper describes a new software package, IMPALA, designed for the complementary procedure of comparing a single query sequence with a database of PSI-BLAST-generated PSSMs. We illustrate the use of IMPALA to search a database of PSSMs for protein folds, and one for protein domains involved in signal transduction. IMPALA's sensitivity to distant biological relationships is very similar to that of PSI-BLAST. However, IMPALA employs a more refined analysis of statistical significance and, unlike PSI-BLAST, guarantees the output of the optimal local alignment by using the rigorous Smith-Waterman algorithm. Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database.
Authors: F M Pearl; N Martin; J E Bray; D W Buchan; A P Harrison; D Lee; G A Reeves; A J Shepherd; I Sillitoe; A E Todd; J M Thornton; C A Orengo Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971
Authors: Frances M G Pearl; David Lee; James E Bray; Daniel W A Buchan; Adrian J Shepherd; Christine A Orengo Journal: Protein Sci Date: 2002-02 Impact factor: 6.725
Authors: A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul Journal: Nucleic Acids Res Date: 2001-07-15 Impact factor: 16.971
Authors: Shashi B Pandit; Dilip Gosar; S Abhiman; S Sujatha; Sayali S Dixit; Natasha S Mhatre; R Sowdhamini; N Srinivasan Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971
Authors: Mark R Chance; Anne R Bresnick; Stephen K Burley; Jian-Sheng Jiang; Christopher D Lima; Andrej Sali; Steven C Almo; Jeffrey B Bonanno; John A Buglino; Simon Boulton; Hua Chen; Narayanan Eswar; Guoshun He; Raymond Huang; Valentin Ilyin; Linda McMahan; Ursula Pieper; Soumya Ray; Marc Vidal; Li Kai Wang Journal: Protein Sci Date: 2002-04 Impact factor: 6.725
Authors: Daniel W A Buchan; Adrian J Shepherd; David Lee; Frances M G Pearl; Stuart C G Rison; Janet M Thornton; Christine A Orengo Journal: Genome Res Date: 2002-03 Impact factor: 9.043