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Old 05-17-2011, 11:47 AM   #1
hxm44
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Location: Cleveland

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Default Online Bisulfite Alignment programs?

Hello,

this is my first time posting here. I was wondering if you could help me find an online free alignment program that could handle short bisulfite alignments.

I do not need to do automated alignment of a large batch of sequences, just align a handful (~20 or so) of 50bp sequences against the whole genome. I know about BSMAP, Novoalign, and other whole genome Bisulfite mapping programs, but I am not able to download any software right now, and just need to check something quickly. E.i. I need something like NCBI Blast that I could use online without downloading anything first.

Thanks a lot!

L.
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Old 05-18-2011, 03:06 AM   #2
fkrueger
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Hi there,

if you just need a one-off answer you can send me a list of sequences to felix.krueger@bbsrc.ac.uk (in FastQ or FastA format) and I can send you the results back via email.

Best,
Felix
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Old 05-18-2011, 05:31 AM   #3
hxm44
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Thanks for the offer, felix!

So there really isn't an online free alignment software?
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Old 05-18-2011, 07:48 AM   #4
C.R.
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Well there is something which is pretty much what you asked for: http://medgen.ugent.be/methBLAST/
I never used it myself, but maybe it is useful for you. But if I were you I would try to get it done with one of the software you mentioned or bismark which Felix offered you.
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Old 05-18-2011, 04:11 PM   #5
ngarg
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Check out the RMAP developed by Andrew Smith at the link below:

http://rulai.cshl.edu/rmap/
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