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Old 08-31-2015, 09:48 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
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I would suggest a Reciprocal Best Blast Hit (RBBH) analysis as your first step in finding candidate homologues. If you have or expect to have lots of gene duplication in either species, then more sophisticated methods/analysis may be needed.

e.g. You could use my script & Galaxy wrapper:
https://github.com/peterjc/galaxy_bl...ocal_best_hits

See also the reference suggested in the help,

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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