Question: Blastp With Just Top Result From Each Organism
1
gravatar for Steve Barratt
5.4 years ago by
Glasgow, UK
Steve Barratt30 wrote:

(My first Q on biostar, forgive any transgressions please!)

I would like to blast a protein/aa sequence and filter(?) my results to include only the top result from each organism. I'm keen to use R or python to accomplish this if they're sensible choices.

Thanks

phylogeny python blast R • 1.3k views
ADD COMMENTlink written 5.4 years ago by Steve Barratt30

what's your output ? does it contain the name of the organisms ?

ADD REPLYlink written 5.4 years ago by Pierre Lindenbaum120k

according to this page: http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html

You can get output from blast+ in the form of "Subject Taxonomy ID(s), Subject Scientific Name(s) and Subject Common Name(s)"

I am sort of asking two questions really: firstly does something exist to do accomplish what I'm after 'off the shelf'? And if 'No.', were I to 'make something' what should my general (or exact!) approach be?

ADD REPLYlink written 5.4 years ago by Steve Barratt30
2

Hi Steve, May not be as complete or clear a reply as you were looking for, but I recently wrote a short, informal web doc, demonstrating two ways to run a blast through R. To my mind, the most flexible/useful is the second, which basically uses blast+ command line through R. While my example demonstrates a nucleotide blast, it would not be difficult for you to alter some arguments to do what you want.

ADD REPLYlink written 5.4 years ago by KKeenan0270

Thanks KKeenan02 I just skimmed your doc, that's really useful. Bookmarked!

ADD REPLYlink written 5.4 years ago by Steve Barratt30
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