Pairwise Sequence Alignment


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Please enter sequence one in FASTA format


Read sequence from local file:



Please enter sequence two in FASTA format

Note: For DNA-Protein or DNA-cDNA comparison, sequence two must
be protein or cDNA sequence


Read sequence from local file:




Run GAP or SIM on protein DNA






If both are DNA or cDNA Sequences

mismatch score

gap open penalty

gap extension penalty

major difference penalty (only for GAP3)

Otherwise

Amino Acid Matrix:

gap open penalty

gap extension penalty

major difference penalty (only for GAP3)

Additional Parameters

gap size for constant penalty


number of local alignment (only for SIM & LAP2)

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