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?
e-mail: Kaj at xray.bmc.uu.se