Protein sequence alignment

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Protein sequence alignment tools include

For finding distant homologs

  • Smith-Waterman
  • FASTA with an appropriate substitution matrix (BLOSUM45, BLOSUM50, BLOSUM62)
  • BLASTP with an appropriate substitution matrix (BLOSUM45, BLOSUM50, BLOSUM62)

For finding homologs based on an alignment

For finding exact or nearly exact matches quickly

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