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The best tips for performing local blastx with XML format output

Hi frineds,

I would like to do local blastx against some databases with the XML format output to import them into Blast2go software, I know blasting with this output format is really time-consuming. Could you please share your helpful tips to do such a blast at a more less time?

Thanks

sequence alignment blast xml output
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updated by Ram Ram • written by seta seta

If there are known nearest species, you can reduce your database also. You still might lose a bit of info, but would still get quick and reliable results as long as you have well annotated species in the database.

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written by Prakki Rama Prakki Rama

2 answers

Use tabular output and map the hits to go terms in the command line? See for example here. What do you need blast2go for?

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written by 5heikki 5heikki

Thanks for your comment. as far as I read blast2go is better choice for gene ontology analysis in non-model organisms. I'll happy if you let me know any other tool for this analysis that works with tabular output. please don't refer to annocript or trinotate

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updated by Ram Ram • written by seta seta

parallelize things: split your input, use a multithreaded blast : http://www.ncbi.nlm.nih.gov/books/NBK279675/

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written by Pierre Lindenbaum Pierre Lindenbaum

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