I should add that you can of course use tBLASTx to generate the comarison data.
Regards Tim On 7/11/06 13:41, "Tim Carver" <[EMAIL PROTECTED]> wrote: > Hi Bala > > No, this is only for DNA sequence comparisons. > > Regards > Tim > > > On 7/11/06 12:02, "BALASUBRAMANIAN GANESAN" <[EMAIL PROTECTED]> wrote: > >> Dear Tim/Julian/users >> Is it also possible to use protein sequence comparisons using this same >> approach? >> Regards >> BALA. >>> ===== Original Message From Julian Parkhill <[EMAIL PROTECTED]> ===== >>> Bala, >>> >>> ACT cannot reconstruct the positional information for the separate >>> sequences within a multiple FASTA file; BLAST reports only the local >>> coordinates for the matches. What you need to do is: >>> >>> 1) Concatenate all the mFASTA sequences into a single sequence for >>> each genome (you can do this from Artemis, using the "Write; all >>> bases" menu) >>> >>> 2) Do the blast comparison with the concatenated sequences >>> >>> 3) Load the original multiple FASTA files into ACT, but use the >>> comparison file from the concatenated sequences. You should see the >>> contigs represented by alternating dark/light brown features, plus >>> the matches for the whole sequences. >>> >>> For the other problem; the set cutoffs only remain for as long as the >>> dialog window is open. Closing the dialog window resets the cutoffs. >>> >>> yours, >>> >>> Julian. >>> >> > > > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
