If you are looking to generate a multiple alignment from a blast report, Nigel Brown's Mview is worth looking into - see http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/ He gives some background on the tiling process in http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/blast/index.html -- Jurgen Pletinckx AlgoNomics NV