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sequence searches

Stuart Yarfitz stuy at u.washington.edu
Sat Dec 16 14:32:19 EST 1995

In article <4amhld$dt6 at oravannahka.Helsinki.FI>, kstenber at cc.Helsinki.FI
(Kaj Stenberg) wrote:

> After trying my way in the web I find it easier to ask.
> I'm looking for a (www-based) search tool that would allow me to do the
> most of these things:
> - input a protein sequense. Search for homology (over some % value) to
> other protein seq, _also translated ORF:s_. The search should allow for
> (even huge) gaps, aligning the sequenses in the "best possible way".
> - get some scoring along the alignment, preferably as a plot of a
> (sliding?) window of i.e. 20 aa.
> - alignment in this way of one search protein against all found over
> some % value of homology.
> And of course: with minimal hands on effort from me.
> Does anyone have a good starting point for me? Is it even possible?

I'm not sure if I understand your question fully, but you might want to
try the Beauty search server at Baylor College of Medicine,
http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/beauty.html.  Beauty
performs a Blast search, which doesn't allow gaps, but it then displays
multiple alignments between your query sequence and protein families to
which it exhibits similarity.  Good Luck.  Stu yarfitz

Stuart Yarfitz
stuy at u.washington.edu
Biological Information Services
Health Sciences Libraries and Information Center
University of Washington

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