Hi Sheila The output of this looks to be a multiple genbank entries in a single file. Artemis therefore just opens the first contig in the genbank file.
Looking at the example you sent me, you can use EMBOSS to create a multiple fasta file: seqret RAST.gbk out.fa and use union¹ to join the contigs together: union -feat -osf RAST.gbk out.embl If you load the multiple fasta sequence (out.fa) into Artemis and then read the output from union (out.embl), File->Read An Entry, then you will see the combined sequence. The advantage of using the multiple fasta is that Artemis will show the separate sequences marked as fasta_record¹ features. Regards Tim On 8/13/12 3:01 PM, "Sheila Patrick" <s.patr...@qub.ac.uk> wrote: > Hi, > > When I try to open a genome .gbk file generated using RAST in Artemis I only > get the first CDS to load and the following error messages- > > while reading from HW RAST.gbk: source can't have genome_md5 as a qualifier > while reading from HW RAST.gbk: source can't have project as a qualifier > while reading from HW RAST.gbk: source can't have genome_id as a qualifier > 13 Aug 12:42:56 - BAM & VCF not visible > > Any advice would be welcome! > Thanks and best wishes > Sheila > > > Chair Society for Anaerobic Microbiology > http://www.clostridia.net/SAM/ <http://www.clostridia.net/SAM/> > > We are recruiting up to 20 Clinical Academic and 15 Academic staff in a range > of clinical and scientific disciplines. For further information, visit > www.qub.ac.uk/sites/QUBJobVacancies/ > <http://www.qub.ac.uk/sites/QUBJobVacancies/> > > > > _______________________________________________ > 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
