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Thanks for your answer. I want my code to be as reproducible as possible and have as little dependencies as possible, so I would rather use remote BLAST than set it up (and expect all my users to set it up) locally. is there any way to BLAST remotely just against the mouse? You said BLAST might not be the best solution - what then? I tried EMBOSS' supermatcher, but that requires local sequences and is excruciatingly slow.... <BR>
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Also, my main concern right now is finding the position of my hits on the genome (chromosome) - could you also tell me something about that?<BR>
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Best,<BR>
Christian<BR>
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On Fre, 2015-02-27 at 21:43 +0000, Peter Cock wrote:
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On Fri, Feb 27, 2015 at 5:42 PM, Horea Chrristian <<A HREF="mailto:h.chr@mail.ru">h.chr@mail.ru</A>> wrote:
<FONT COLOR="#737373">> Hi again, I am trying to align a sequence to the mouse genome,</FONT>
<FONT COLOR="#737373">> I am currently doing it thus ... [BLAST against nt database].</FONT>
BLAST may not be the best tool for this (depending on how
many and how long your sequences are it could be fine).
Moreover, if you want to align against the mouse, why do
an expensive (slow) BLAST against the entire nt database
(most of which is non-mouse sequences).
If you are happy to run BLAST locally, setup a BLAST
database of the mouse genome only, and BLAST against that.
Peter
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