Thanks for your suggestions. I will add this to the documentation, possibly as FAQs for ACT.
Regards Tim On Mon, 6 Nov 2006, BALASUBRAMANIAN GANESAN wrote: > Julian > thanks for your suggestions. > My comparison looks fine now. I could not find this anywhere on the manual for > ACT. May be I did a > poor job in trying to look for it in partcular. > Naive users like me would benefit from an explicit instruction, despite the > fact this should be somewhat > intuitive. > Thank you Tim and Julian > BALA. > P.S. We have been using MUMmer to look at genome synteny. MUMmer does > analogous alignments > functions and has an even simpler output format. I would like to suggest a > look at using MUMmer > output for genome alignments also in ACT future versions. However I assume > that an artificially create > text file that is in any of the current comparison file input formats will > work just as well. > > > >===== 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. > > > > > >On 6 Nov 2006, at 16:50, [EMAIL PROTECTED] wrote: > > > >> Dear Julian > >> I am comparing them using multiple fasta sequences within a single > >> file > >> that represent one contig, such as a chromosome or plasmid. > >> Do I need to do single contig sequences? I did not think so. > >> Regards > >> BALA. > >> > >> On Mon, 6 Nov 2006, Julian Parkhill wrote: > >> > >>> Dr. Ganesan, > >>> > >>> are these genomes represented as single sequences, or are they > >>> multiple FASTA files? > >>> > >>> yours, > >>> > >>> Julian. > >>> > >>> On 5 Nov 2006, at 08:23, BALASUBRAMANIAN GANESAN wrote: > >>> > >>> Hello > >>> I am using ACT v5 for the Mac to look at a two-genome comparison to > >>> start off > >>> with. > >>> Many features seem to not work such as score cutoff, percent ID > >>> cutoff are > >>> never apllied or saved after > >>> setting them. The sequence lock works totally at random. > >>> But my main problem is that the comparison view shows only the > >>> comparisons for > >>> the first 5-6k bases for > >>> 2.5 Mb genomes. Why is this the case? > >>> I am running OSX-10.4.3 and using blastall text o/p directly as the > >>> comparison > >>> file generated by the > >>> blastn option using -m 8 to generate a tabular output. I had the > >>> display > >>> problem after trying the unix > >>> version of ACT on my Mac also. I recreated my blast comparison > >>> without a > >>> specified e-value and still had > >>> the problem. > >>> What can possibly cause this issue? > >>> Kindly help. > >>> > >>> Thank you, > >>> Regards, > >>> > >>> Dr. BALASUBRAMANIAN GANESAN > >>> Research Group Leader - BioSystems Modelling > >>> Service Group Leader - Bioinformatics > >>> CENTER FOR INTEGRATED BIOSYSTEMS > >>> UMC-4700 > >>> UTAH STATE UNIVERSITY > >>> LOGAN UT-84322. > >>> US OF A. > >>> > >>> > >>> _______________________________________________ > >>> Artemis-users mailing list > >>> [email protected] > >>> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > >>> > >>> Julian Parkhill > >>> Head of the Pathogen Sequencing Unit, > >>> The Sanger Institute, > >>> Wellcome Trust Genome Campus, > >>> Hinxton, Cambridge, CB10 1SA, UK > >>> > >>> Visiting Professor in Microbial Genomics, > >>> University of Oxford > >>> > >>> Tel: +44(0)1223 494975, Fax: +44(0)1223 494919 > >>> http://www.sanger.ac.uk/Projects/Pathogens > >>> http://www.sanger.ac.uk/Teams/faculty/parkhill > >>> > >>> > >>> > >> > > > >Julian Parkhill > >Head of the Pathogen Sequencing Unit, > >The Sanger Institute, > >Wellcome Trust Genome Campus, > >Hinxton, Cambridge, CB10 1SA, UK > > > >Visiting Professor in Microbial Genomics, > >University of Oxford > > > >Tel: +44(0)1223 494975, Fax: +44(0)1223 494919 > >http://www.sanger.ac.uk/Projects/Pathogens > >http://www.sanger.ac.uk/Teams/faculty/parkhill > > The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
