[Bio-software] Re: Motif Finding programs / algorithms

Kevin Karplus via bio-soft%40net.bio.net (by karplus from cheep.cse.ucsc.edu)
Wed Oct 25 17:34:22 EST 2006

On 2006-10-24, mark <mkazmierski from gmail.com> wrote:
> I am a new in bioinformatics field. Presently I am looking at good
> description (algorithms / open software) about finding motifs for
> DNA/RNA strings. I.e. my task is just to explore the problem of finding
> the longest motifs (with possible mutation) in the specified number of
> strings. Would be grateful for any information about that problems
> (tutorials / books / source codes / descriptions / etc.).

For a real brief intro, look at the Wikipedia article "Sequence
motif", which points to MEME and mentions other methods.
That should at lesat get you keywords for searching article databases.

There was a review article
	Wyeth W. Wasserman, William Krivan
	In silico identification of metazoan transcriptional regulatory regions
	Naturwissenschaften	Volume 90, Number 4 / April, 2003	156-166
but I've not read it and don't know if it is the best review.

Kevin Karplus 	karplus from soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors & Chair of Education Committee, ISCB)
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