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Old 08-26-2013, 01:12 AM   #2
mbayer
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Location: Dundee, Scotland

Join Date: Mar 2009
Posts: 29
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Hi Petrichor,

by default BLAST hits with multiple HSPs to the same subject are sorted by bit score in descending order, i.e. the best (and usually longest) HSP is topmost.

Here is what I have done in the past to extract these:

1. Generate tabular BLAST output (use "-outfmt 6" option in BLAST+ executables)
2. Load this into Excel or whatever you use to view spreadsheets
3. Remove duplicates based on the subject column. This should get rid of any secondary HSPs for each subject, and leave only topmost ones, as the output is already sorted. If there are more than two HSPs per subject you may need to repeat this until you are left with just one each.

cheers

Micha
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