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). Ryan _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
