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 >>> Artemis-users@sanger.ac.uk >>> 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 _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
