Ryan Golhar wrote: > I have a BLAST alignment: query sequence and database sequence. > > The alignment is only showing the HSP from the blast output as expected, > however I want to build an alignment of the entire database sequence > against my query sequence. > > I tried using needle from EMBOSS, however its aligning the sequences > completely different than BLAST does. What I'd really like is a way to > anchor the alignment based on the BLAST HSP. Does anyone know how to do > this, or what tool(s) will allow me to do this?
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. 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. We do have at least one EMBOSS application that does something similar (finds all long perfect matches and interpolates) - we just need to reuse the interpolation code which is basically doing a global alignment of the bits in between. That also tackles the problem of choosing which non-compatible initial matches to use. Hope that helps, Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
