blastn for matching small sequences
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8.8 years ago

hello, i stuck with the blast command, see when i do blastn for 300 bp long seq then it retains result but when i do blastn for 20-25 nucl seq then it retain no result. do you have any idea why so it is? i want to blast small sequences with my local database.

blast • 1.3k views
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8.8 years ago
zizigolu ★ 4.3k

http://www.ncbi.nlm.nih.gov/blast/html/BLASThomehelp.html in Search for short, nearly exact sequences section you may could find some clues

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