Hi Filipe Thanks for your suggestions. Currently those are not possible, so I shall take a look. However, having separate files may not be possible at the moment.
The flag for memory used in the PSU is usually set to: -mx1500m If you have this memory available to you, you could start with that. Regards Tim On 4/2/08 15:39, "Filipe Garrett" <[EMAIL PROTECTED]> wrote: > > Hi all, > > This new features seem just what I was looking for. However I still have some > doubts: > > Is there a way to set the "Frame Line Features..." options at start-up > (through > the options file)? > > I've noticed that relating sequence with feature is only possible when the > FASTA > sequences are inside the GFF file. This is not so handy when your handling big > files, such as entire genomes. Is it possible to relate both things when you > add > each entry separately? > > I also have some memory problems when loading an entire genome + GFF > annotations. How much memory do you think it would be necessary for artemis to > run? 2Gb? > > A minor change, when loading a multi-FASTA file, would also come in hand. > Artemis, currently, interprets the whole '>' string as the sequence ID. It > would > be nicer if it was just until the first SPACE (the standard behaviour). That > way > it is possible to add some description. > > thanks in adv, > FG > > > Tim Carver wrote: >> 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 _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
