sequence searches

[Frank van de Loo]

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.

If I were to do the same thing, I would first find homologous sequences 
with BLAST at NCBI:
http://www.ncbi.nlm.nih.gov/
Then I would retrieve the sequences and do further alignments with a 
program on my PC, such as MACAW, also from NCBI (in their FTP 
repository).

Not to say there aren't better ways.  Good luck,
Frank van de Loo.