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Old 02-10-2017, 08:33 AM   #8
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
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Here's a BLAST RBH tool I wrote earlier in Python, which does consider duplicates and gives warnings about them:
https://github.com/peterjc/galaxy_bl...h/blast_rbh.py

It has a Galaxy wrapper but you can ignore that, other than perhaps reading the help text included it it - which suggests thinking about setting minimum identity and minimum alignment lengths and reading this paper:

Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
or How To Use Sequence and Structure Information To Predict Protein
Function. PLoS Comput Biol 4(10): e1000160.
http://dx.doi.org/10.1371/journal.pcbi.1000160
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