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How do I perform a similarity search with a shor...

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How do I perform a similarity search with a short peptide/nucleotide sequence?

There is a special page with pre-set parameters for searching with short sequences. You can access this page by clicking the "Search for short nearly exact matches" link on the main BLAST web page.

Essentially for these searches, the Expect value has been increased and the word size decreased to optimise for short hits which generally score a large E value require smaller word sizes to initiate formation of the HSP for extension. In addition, for proteins, the matix "PAM30" becomes the default which optimises hits to smaller sequences which have a lower percentage of evolutionary drift in general.

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