Help! Software to extract motif from alignment produced by CLUSTAL W.
phains at NOSPAMproteome.org.au
Sun Jan 17 17:52:33 EST 1999
You can try PRINTS at:
or BLOCKS at: http://blocks.fhcrc.org/blocks/blockmkr/make_blocks.html
I don't think either are available for the PC but both can be used easily over
the web. I have not used either so I cannot comment further on how good or
otherwise they are.
Prosite will run under Genedoc (W95, NT or 3.1):
http://www.cris.com/~ketchup/genedoc.shtml but you will need to get the
PROSITE database: http://expasy.proteome.org.au/cgi-bin/lists?prosite.get
follow the instructions and away you go. Genedoc is also a great tool for
preparing and analysing aligned sequences. Additionally, with Genedoc you can
input MEME data and automatically colour the sequences accordingly. I'd give
MEME another go if I were you.
Hope this helps, Peter.
>So, what I prefer is I send an alignment in to it, and it give out motif(highly
>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?
I'm afraid I don't have a clever saying to put here.
Remove NOSPAM to e-mail me.
Peter Hains Ph. +61 2 9850 6216
Australian Proteome Analysis Facility Fax. +61 2 9850 6200
Level 4 Building F7B
Macquarie University, Sydney 2109
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