sequence searches

[Stuart Yarfitz]

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
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