I would like to align ~15 DNA sequences of 1-2kb, then assess the degree of homology across the alignment using a sliding window. It will be very laborious to do this manually, even using quite large jumps in the windows. Is there a facility to do such analysis automatically with the Clustal Omega tool (or other tool)? Many thanks Catherine Merrick
Sorry, just a pet peeve, but "degree of homology" makes no sense. Either a sequence is homologous, or it is not. I.e. either they share a common ancestor or they do not! check here for a way to get you started.
Thank you. (I take the point re semantics, but it doesn't stop biologists in common parlance saying things like 'highly homologous'!). I think I now have various ways of getting the measures I need (entropy scores), inc. this http://evolve.zoo.ox.ac.uk/Evolve/SHiAT.html and this https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl ... so I need to bin them appropriately across the alignment.