Apr 1, 1988

Improved tools for biological sequence comparison

Proceedings of the National Academy of Sciences of the United States of America
W R Pearson, D J Lipman

Abstract

We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternativ...Continue Reading

  • References9
  • Citations5408

References

  • References9
  • Citations5408

Citations

Mentioned in this Paper

Computer Software
Emergency Care Information Systems
Computer Programs and Programming
Globin
Homologous Sequences, Nucleic Acid
Polypeptides
T-Cell Receptor
Transforming Growth Factors
Metazoa
DNA Sequence

About this Paper

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