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Old 08-06-2012, 09:15 PM   #1
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Location: Australia

Join Date: Sep 2011
Posts: 4
Default how do i do a bitscore cut off in blastn in blast+

How do i do a bit score cut off in blastn in blast+?

It can do an evalue cut off but if i search in different databases that will correspond to a different scoring hit. I want a consistent score cut off regardless of database size.


-min_raw_gapped_score <Integer>
Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages

But that doesn't seem like a simple cut off on final results. Nothing seems like it fits?
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