[EMBOSS] Align 12bp DNA back to genome

[Giovanni Marco Dall'Olio]

On 2/6/09, Lapointe, David <David.Lapointe at umassmed.edu> wrote:
> Aengus,
>
>  You might try looking here for other software. Maq, soap, rmap, etc are
>  relatively fast but still time-consuming.
>
>  http://seqanswers.com/forums/showthread.php?t=43
>
>  David
>
>  -----Original Message-----
>  From: emboss-bounces at lists.open-bio.org
>  [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Aengus Stewart
>  Sent: Friday, February 06, 2009 11:11 AM
>  To: emboss at lists.open-bio.org
>  Subject: [EMBOSS] Align 12bp DNA back to genome
>
>
>  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

I think 12 bp is too short to obtain good results.
How much big is the genome that you want to search? Have you
calculated the probability that your 12 bp sequences match to a random
location in the genome? Or to two distinct positions?
The human genome is not homogenously  sequenced: there are still
regions full of errors and of 'N's. What if one of your sequences
falls in such a zone?
Moreover, the genomic sequence that you are working with could not be
the same as the one from which you have extracted your seqs.


>
>  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
>
>  --
>  -----------------------------------------------------------------------
>  Aengus Stewart
>  Head of Bioinformatics and BioStatistics
>  Bioinformatics and BioStatistics               Tel: +44 (0)20 7269 3679
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