Hi Jack Artemis is not really meant as a conversion tool between formats and in particular EMBL/GenBank to GFF, although it will have a go. You could try EMBOSS (seqret) to convert. However, it sounds like you have multiple fasta records in your file which may cause problems if you are writing out embl files. So you may want to try writing the sequence out (File->Write->All bases). Open this single sequence file and then read your annotation into the sequence entry. Then write out the file as EMBL.
Regards Tim On 10/21/10 12:26 PM, "Jack van de Vossenberg" <j.vandevossenb...@science.ru.nl> wrote: > Addition: > For Artemis export to GFF, I changed "fasta_record" to "source", which > is a Feature Key in standard nomenclature*, and added the mandatory > fields /organism= and /mol_type=, but every time I get a message that > the source field cannot be exported. > > Is that normal behaviour? Can anyone tell what goes wrong? > > Cheers, Jack > > * http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html > > On 10/21/2010 10:27 AM, j.vandevossenb...@science.ru.nl wrote: >> Dear all, >> >> I have annotated genome data in Artemis, and I would like to import the >> result of that annotation into CLC Bio Genomics Workbench >> (http://www.clcbio.com/). >> >> I tried direct import, selected all entries and exported from Artemis to >> EMBL, Genbank and Sequin. None of these were recognized by CLC, even >> though it should be able to import many file formats >> (http://www.clcbio.com/index.php?id=426). >> I tried SFF, which does not include sequence data. So I used a separate >> sequence file, the contigs concatenated into one large fasta sequence. CLC >> has a SFF import filter, which is very picky about the sequence names >> (read CLC SFF import manual). I managed to let it import SFF, but I did >> not see any annotation at all, I think because all ORFs are named artemis >> ("gff_seqname artemis"). Contig names are lost in SFF, so this option may >> import all annotated genes, but lose contig info. SFF does not recognize >> "fasta record" so I should rename this into something (but what? I tried >> "contig", "source", but the GFF file keeps on using ORFs only, all named >> "gff_seqname artemis"). >> >> Does anyone have experience with this? I thought of using another program >> as intermediate to convert Artemis data into CLC readable data. >> >> Thanks for your help, Jack >> >> >> _______________________________________________ >> 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 _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
