Arvind,

Like bobf I think you should generate your own program to do what BIMAS does, but from personal experience. That server crashed on me frequently this March when I was doing a project on it. It won't take much of your time to do that.
If I can find the program my group wrote, I can put it here, but I rather doubt I'll be able to reach it anytime soon.

On an aside, (but important, me thinks) if you are going to use BIMAS, then please use FASTA format, it's much safer. BIMAS does not read raw sequences less than a specific length (111 bps, I think). Your sample data has only 147.

UPDATE: (reply to Arvind): It isn't too tough. :) and I'm still in college.

In reply to Re: bioinformatics problem by sarani
in thread bioinformatics problem by mutatedgene

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