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IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis

Part 4. Bioinformatics

4.3. Protein Function and Annotation

Basic Techniques and Approaches

  1. Yuri I. Wolf

Published Online: 15 JUL 2005

DOI: 10.1002/047001153X.g403411

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Wolf, Y. I. 2005. IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.3:39.

Author Information

  1. National Institutes of Health, Bethesda, MD, USA

Publication History

  1. Published Online: 15 JUL 2005

Abstract

Pairwise sequence comparison works well if the sequence similarity is high; as the similarity decreases, alignment scores become less and less reliable. Profile-based approaches allow to extend the analysis into the “twilight zone”. Several NCBI tools – PSI-BLAST, IMPALA, and RPS-BLAST – can be used to iteratively build position-specific scoring matrices and use them in direct (query profile against a sequence database) and reverse (query sequence against a profile database) similarity searches.

Keywords:

  • PSI-BLAST;
  • IMPALA;
  • RPS-BLAST;
  • sequence similarity search;
  • profile search;
  • profile library