Online Bisulfite Alignment programs?

[hxm44]

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.

[fkrueger]

Hi there,

if you just need a one-off answer you can send me a list of sequences to [email protected] (in FastQ or FastA format) and I can send you the results back via email.

Best,
Felix

[hxm44]

Thanks for the offer, felix!

So there really isn't an online free alignment software?

[C.R.]

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.

[ngarg]

Check out the RMAP developed by Andrew Smith at the link below:

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