Hi Malcolm I think the normal trick is to create a single fasta from Artemis by File->Write->All Bases->FASTA format. This then gets them on the correct coordinate system for your query.
The GFF multiple contig thing is a problem. It only really copes with a single sequence. I haven't loaded GFFs into chado that have multiple contigs and tried it with Artemis. However we do plan on soon being able to handle that sort of situation and concatenate contigs together. Regards Tim On 2/26/09 3:58 PM, "Cook, Malcolm" <m...@stowers.org> wrote: > I read in the artemis manual about the "feature keys 'fasta_record' or > 'contig'" (which are) "create when a multiple fasta sequence file is read in". > > Indeed this works - I am able to load such a fasta file holding multiple 300 > contigs generated by an assembly. > > However, I find that when I load extenrally generated blast results where the > subject (or query) sequences are the same contigs, the blast table (-m 8) when > loaded into Artemis are not (re)interpreted with respect to the appropriate > contig. > > Similarly, if I load externally generated GFF features (i.e. output from > exonerate and fgenesh) that have the my same contig identifiers in column 1, > they are not applied to the corresponding contig, but rather to what appears > to be a single entry gained by linearizing/concatenatig the individual reads. > > Is there some way I should be using Artemis to allow loading multiple contigs > and corresponding annotation of each contigs for simultaneous visualization? > > Perhaps I should rather be loading a Chado database and performing annotation > against it? > > Andy advice in using Artemis toward my end of allowing manual curation of > annotation of upwards of 300 contigs would be welcome. > > Thanks! > > Malcolm Cook > Stowers Institute > > > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
