• Publications
  • Influence
Improved tools for biological sequence comparison.
  • W. Pearson, D. Lipman
  • Biology, Medicine
    Proceedings of the National Academy of Sciences…
  • 1 April 1988
TLDR
Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
Rapid and sensitive protein similarity searches.
TLDR
An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases and increases sensitivity by giving high scores to those amino acid replacements which occur frequently in evolution.
Rapid and sensitive sequence comparison with FASTP and FASTA.
  • W. Pearson
  • Biology, Medicine
    Methods in enzymology
  • 1990
TLDR
FASTA and FASTP were designed to identify protein sequences that have descended from a common ancestor and they have proved very useful for this task, but it is not clear that NWS-based programs would be more successful in finding distantly related members of the G-protein-coupled receptor family.
Flexible sequence similarity searching with the FASTA3 program package.
  • W. Pearson
  • Computer Science, Medicine
    Methods in molecular biology
  • 2000
The FASTA3 and FASTA2 packages provide a flexible set of sequence-comparison programs that are particularly valuable because of their accurate statistical estimates and high-quality alignments.
Comparison of DNA sequences with protein sequences.
TLDR
FASTX and FASTY are used to scan the Mycoplasma genitalium, Haemophilus influenzae, and Methanococcus jannaschii genomes for unidentified or misidentified protein-coding genes and are found to be quite accurate, except when an out-of-frame translation produces a low-complexity protein sequence.
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
  • W. Pearson
  • Biology, Medicine
    Genomics
  • 1 November 1991
The sensitivity and selectivity of the FASTA and the Smith-Waterman protein sequence comparison algorithms were evaluated using the superfamily classification provided in the National Biomedical
Empirical statistical estimates for sequence similarity searches.
  • W. Pearson
  • Mathematics, Medicine
    Journal of molecular biology
  • 13 February 1998
The FASTA package of sequence comparison programs has been modified to provide accurate statistical estimates for local sequence similarity scores with gaps. These estimates are derived using the
Effective protein sequence comparison.
  • W. Pearson
  • Biology, Medicine
    Methods in enzymology
  • 1996
TLDR
Although there are several different comparison programs available (e.g., BLASTP, FASTA, SSEARCH, and BLITZ) that can be used with different scoring systems, the following search protocol should identify homologous sequences whenever they can be found.
Comparison of methods for searching protein sequence databases
  • W. Pearson
  • Mathematics, Medicine
    Protein science : a publication of the Protein…
  • 1 June 1995
TLDR
Search sensitivity with either the Smith‐Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45–55, and optimized gap penalties instead of the conventional PAM250 matrix.
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