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Hi again Peter,<BR>
<BR>
Thanks for the answer:<BR>
<BR>
> BLAST alignments include the start/end coordinates of the match on both the query sequence and the match/hit sequence.<BR>
<BR>
Is there any convenient way to access these values from within biopython? Quite frankly I can't even find them by looking at the XML <A HREF="https://bpaste.net/show/3c2d54393feb">https://bpaste.net/show/3c2d54393feb</A> (the output is huge, this is just the part that fit into my console).<BR>
<BR>
So, can you show me how to get those values?<BR>
<BR>
Best,<BR>
Christian<BR>
<BR>
<BR>
<BR>
On Mon, 2015-03-02 at 13:24 +0000, Peter Cock wrote:
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Hi Horea,
On Sat, Feb 28, 2015 at 5:47 AM, Horea Chrristian <<A HREF="mailto:h.chr@mail.ru">h.chr@mail.ru</A>> wrote:
<FONT COLOR="#737373">> Thanks for your answer. I want my code to be as reproducible as possible and</FONT>
<FONT COLOR="#737373">> have as little dependencies as possible, so I would rather use remote BLAST</FONT>
<FONT COLOR="#737373">> than set it up (and expect all my users to set it up) locally. is there any</FONT>
<FONT COLOR="#737373">> way to BLAST remotely just against the mouse? You said BLAST might not be</FONT>
<FONT COLOR="#737373">> the best solution - what then? I tried EMBOSS' supermatcher, but that</FONT>
<FONT COLOR="#737373">> requires local sequences and is excruciatingly slow....</FONT>
If you don't want to install any local software, databases or
copy of the mouse genome, then NCBI BLAST is probably
quite a good solution (especially given the low volume of
data - just two queries).
<FONT COLOR="#737373">> Also, my main concern right now is finding the position of my hits on the</FONT>
<FONT COLOR="#737373">> genome (chromosome) - could you also tell me something about that?</FONT>
<FONT COLOR="#737373">></FONT>
<FONT COLOR="#737373">> Best,</FONT>
<FONT COLOR="#737373">> Christian</FONT>
BLAST alignments include the start/end coordinates of the match
on both the query sequence and the match/hit sequence.
Peter
</PRE>
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