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Can I use BLAST to compare to two or m...

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Can I use BLAST to compare to two or more sequences in a multiple sequence alignment?

You can use the BLAST 2 Sequences service to compare two nucleotide or two protein sequences against each other using the Gapped BLAST algorithm. The this will allow you to perform a BLAST search between the two sequences allowing for the introduction of gaps (deletions and insertions) in the resulting alignment. Remember that BLAST is a "local" alignment program and does not make global alignments between sequences to calculate total percent homologies.

To compare one sequence against a specific sequence or set of sequences, you can also use a separate multiple sequence alignment program. There are many such software tools available to do this. You may also be interested in checking out other molecular biology web sites, such as those mentioned in the "Other Molecular Biology Resources" section at the end of this FAQ.

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