IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices

• Alejandro A.Schäffer

• Yuri I.Wolf

• Chris P.Ponting

• Eugene V.Koonin

• L. Aravind

• Stephen F.Altschul

抄録

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. Availability: The IMPALA source code, the wolf1187 database, and the aravind105 database are freely available from the NCBI ftp site ncbi.nlm.nih.gov. The databases may be found in the subdirectory ftp://ncbi.nlm.nih.gov/pub/impala. The source code is in ftp://ncbi.nlm.nih.gov/toolbox/ncbi˙tools. Some IMPALA executables for different implementations of UNIX are in ftp://ncbi.nlm.nih.gov/blast/executables. IMPALA has been added as a search option on the Blocks Database Server (http://blocks.fhcrc.org/blocks/impala.html)using a library of PSSMs derived from the BLOCKS database. Contact: [e-mail]

収録刊行物

• Bioinformatics

  Bioinformatics 15 (12), 1000-1011, 1999-12-01

  Oxford University Press (OUP)

キーワード

• Computational Mathematics
• Computational Theory and Mathematics
• Computer Science Applications
• Molecular Biology
• Biochemistry
• Statistics and Probability

詳細情報

• CRID: 1362825896377417216
• NII論文ID: 30018395192
• DOI: 10.1093/bioinformatics/15.12.1000
• ISSN: 13674811
• ISSN: 13674803
• Web Site: https://academic.oup.com/bioinformatics/article-pdf/15/12/1000/48835192/bioinformatics_15_12_1000.pdf
• データソース種別:
  • Crossref
  • CiNii Articles