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Protein domain/function prediction

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Dear colleagues,
I have a series of predicted ORFs from some novel transcripts we detected.
I want to make some predictions on the putative function based on the present domains and homology.
Are there any tools that you would recommend?
And what are potential pitfalls?
asked May 25, 2016 in Bioinformatics by falko.hofmann (400 points)

1 Answer

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If you want to find domains, I would suggest trying Prosite. It has a whole list of protein domains which you can search through either a web interface or download and use on the commandline. I used it to find all the known domains in a number of proteins which it did rather well.

answered Sep 1, 2016 by jason.bosch (220 points)