Hi Chris You need to use something like the EMBOSS application 'union'. Separate them into individual EMBL files and concatenate them into a single EMBL entry file (use the -feature option and -sformat embl).
Regards Tim On 20/3/08 15:18, "Chris Knight" <[EMAIL PROTECTED]> wrote: > I am having difficulties opening an EMBL file in Artemis: > > The file in question contains a single genome divided into several > hundred contigs. These contigs are listed in the file I have as separate > entries, each with a separate sequence (SQ) entry- I'd like to read them > all in (and have them appear as separate contigs), however I can only > persuade Artemis to read the first contig. > > The separation between the contigs at present is a line containing only > two forward slashes between the end of the preceding contig's sequence > entry (SQ section) and the beginning of the next contig (ID section). > > I've tried manipulating the file with Readseq v 2.1.26, which will > happily output everything to fasta format, which allows me to read all > the contigs into Artemis correctly. However, I then lose the annotation > in the embl file. Readseq will separate out the annotation into a > separate .fff file (by using -unpair=1), however, this file is in gff > format v2 and it doesn't seem to read in as an entry into artemis which > wants gff v3 (or rather the file reads, but appears as an empty entry). > > Apologies if I've missed something obvious, but any help much appreciated, > > Thanks, > > Chris > > I'm using Artemis release 10 on a Mac running OSX 10.5.2 _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
