[EMBOSS] Align 12bp DNA back to genome

[Aengus Stewart]

Hi all,

This isnt an EMBOSS question per se but I thought it would go to the right audience.

After trimming a bunch of illumina reads I have sequences that are 12bp long and "we" want to find 
their genomic location

Before anyone even says "Why do you want to do that?" can I suggest

1) Treat it as a hypothetical case
2) because the scientist who asked me wants it

:-)

I have both a perl regex and fuzznuc running now for oh about a week..........

I have also attempted to build/configure/run without success

maq
soap
blat

So can anyone suggest anything else to try (probably I have missed the obvious) before the regex and 
fuzznuc finish?

This completes the Friday pm puzzler........



Cheers
Aengus

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Aengus Stewart
Head of Bioinformatics and BioStatistics
Bioinformatics and BioStatistics               Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
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