Anthony Barbet wrote: > > I have been using ACT with unfinished microbial sequence files > downloaded from TIGR. I have tried using these files ( each downloaded > file consisting of multiple individual sequence files of different > contigs) directly with the blastall command "formatdb" and then with > the blast program itself and the "-m 8" flag to output a comparison file > for ACT. This generates a useful line in the ACT display that shows the > contigs in different colours and the contig junctions, but the > comparison itself is incorrect. To get the correct comparison I have > been reformatting the downloaded TIGR file (which appears to be multiple > fasta format files anyway) as a single fasta file output from ARTEMIS > before using "formatdb" . Then the comparison file is good but I lose > the display of contig junctions. For my purposes I can keep two ACT > windows open, one showing the contig junctions and one the blast > comparisons. This works, but is there a better way to look at unfinished > sequence with ACT? > Tony Barbet > University of Florida
Tony, This is exactly the way that we work with unfinished sequences in ACT or Artemis; write out the multiple sequences as a sigle file to do all the analysis/comparisons etc on that. All you need to do then is load in the original multiple sequence file, and then the comparisons/analysis done with the single sequence file. Artemis/ACT will then mark up the boundaries of the individual subsequences, and show the comparisons/analyses relative to the full sequence coordinates. Julian. -- Dr. Julian Parkhill The Sanger Institute mailto:[EMAIL PROTECTED] Wellcome Trust Genome Campus Tel: +44(0)1223 494975, Fax: +44(0)1223 494919 Hinxton http://www.sanger.ac.uk/Projects/Microbes Cambridge http://www.sanger.ac.uk/Users/parkhill CB10 1SA, UK
