Help! Software to extract motif from alignment produced by CLUSTAL W.

xietao xietao at SUNM.SHCNC.AC.CN
Fri Jan 15 00:19:07 EST 1999


>I have used and would recommend MEME, available via a Web interface at: 
>http://www.sdsc.edu/meme/meme/website/
>If you're really keen, the maker of Genedoc has ported the MEME code to 
>run under Windoze DOS mode available at: ftp://ftp.netcom.com/pub/ka/karl/
>Regards, Peter.

Dear Peter:
Thank you for your reply!

Actually, I have used MEME before. But it need your give it several parameters: 
Short or Wide motif, how many you want to get etc. And, it did not use Alignment methods.

So, what I prefer is I send an alignment in to it, and it give out motif(highly conserve)
region. I think PROSITE and BLOCKS are make in this way. But I can not find a suitble software 
that can run under my PC and be merged into a batch work.

Could you give me more comments?

Thank you!

Sam 
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Xie Tao
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Shanghai Institute of Biochemistry, Academia, Sinica
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