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Pairwise Sequence Alignment (PSA) is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).

Important Note

  • PSA tool algorithms are NOT intended to produce genome synteny maps.
  • We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

Type REST ServiceDescription
Global AlignmentEMBOSS needle Needleman-Wunsch global alignment using EMBOSS needle.
EMBOSS stretcherMyers and Miller global alignment using EMBOSS stretcher.

Local Alignment

EMBOSS waterSmith-Waterman local alignment using EMBOSS water.
EMBOSS matcherWaterman-Eggert local alignment using EMBOSS matcher.
LALIGNHuang and Miller sim local alignment using lalign.
Genomic AlignmentGeneWiseComparing a protein sequence to a genomic DNA sequence.
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