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

[Peter Hains]

Sam,

You can try PRINTS at: 
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS/PRINTS.html
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
> 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!




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Peter Hains				Ph. +61 2 9850 6216
Australian Proteome Analysis Facility	Fax. +61 2 9850 6200
Level 4 Building F7B			
Macquarie University, Sydney 2109