On Mar 27, 2006, at 8:03 PM, Ryan Golhar wrote: > Hi Peter, > >> You are quite right that EMBOSS may align the sequences completely >> differently - unless the HSPs are very significant and cover most >> of the sequence this will be true of any attempt to simply realign. >> There has to be some way to pass on the HSPs as fixed positions, >> as in the BioPerl solution. > > I looked at a bioperl method, but can't seem to find something that > will > accomplish this. > >> However, it could make a nice EMBOSS application - the only question >> would be how you would like to specify the HSPs. Perhaps we could read > >> BLAST output (in some specified format), or perhaps some other way to >> give the input alignments. > > Yes, I agree. I suppose the best way would be to specify the two > sequences and the blast output. The application could then construct > an > alignment based on a particular HSP (probably the first one, or > whatever > the user specifies). >
Have you tried this: http://bioweb.pasteur.fr/seqanal/interfaces/seqsblast.html It is based on bioperl. check "Get HSP" option (you can even extend it). Best, -- Catherine Letondal -- Institut Pasteur -- Computing Center _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
