Hi Filipe It sounds like you are better off using the "Frame Line Features..." option. This allows you to define what features you want displayed on the frame lines. I think the other option is there for convenience and for when it is suitable.
In the development version of Artemis you can have GFF3 with multiple sequences and the coordinates for the features relating to each (as below). E.g. ## gff-version 3 ## contig1 foo CDS 3 32 . - . ID=cds1;colour=8 contig1 foo3 CDS 3 32 . + . ID=cds3;colour=8 contig2 foo2 CDS 17 19 . + . ID=cds2;colour=2 ### ##FASTA >contig1 gatcccaactgctcctaccgtcattggatccagcggcgttccctcttccttctccaccgt tccttctagcagcggcgtcaagagctctaccaagactgcctcgaccgcaactgccaccga >contig2 gatcccaactgctcctaccgtcattggatccagcggcgttccctcttccttctccaccgt tccttctagcagcggcgtcaagagctctaccaagactgcctcgaccgcaactgccaccga Hope this helps. Regards Tim On 1/2/08 16:17, "Filipe Garrett" <[EMAIL PROTECTED]> wrote: > Hi all, > > I've been trying to use Artemis with a recent Ensembl files from Anopheles > (3.46). > > However, some things came to my atention. > When I activate the "All features On Frame Lines" every feature is depicted on > its correspondent lane. But why are exons also places on the frame lines? The > exons don't have any frame! Shouldn't the frameless features be maintained on > the central lines (or on a non-frame line)? > The same thing happens when adding a multi-FASTA file. A concatenated sequence > is loaded and several features, labelled "fasta_record", are created. Again > this > features are placed as having frame! > Is this a bug or am I forgetting something? > > Another thing that I've noticed is that there is no use for the "seqname" > field > in the GFF files. When placing features only the position and strand are taken > into account, with all of them being placed in its positions but counting from > the beginning of the concatenated sequence. > Is there a way to link the "seqname" field with the "fasta_record" feature so > that each feature is placed on the correct sequence? The idea would be to load > a > single GFF with the annotations for all the sequences present in a > multi-FASTA. > > SEQ1 EMBL atg 103 105 . + 0 > SEQ1 EMBL cds 103 171 . + 0 > SEQ1 EMBL stop 172 174 . + . > > SEQ2 EMBL atg 173 175 . + . > SEQ2 EMBL cds 173 258 . + . > SEQ2 EMBL stop 259 261 . + 0 > > > thanks in adv, > FG > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
