IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis
Part 4. Bioinformatics
4.3. Protein Function and Annotation
Basic Techniques and Approaches
Published Online: 15 JUL 2005
Copyright © 2005 John Wiley & Sons, Ltd
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.
- Published Online: 15 JUL 2005
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.
- sequence similarity search;
- profile search;
- profile library