> I faced this problem a little while ago, and had to ask genbank to do > the conversion for me! Can you hazard a guess > as to why Genbank makes this so difficult?
No, I was also wondering why the sequin tool can't read one of the common formats. > Genbank put forward > the .asn format as a > standard format yet they don't offer a conversion utility (e.g. from > genbank or embl format to > .asn). I haven't tried the program mentioned below. How long has it > been available? I wrote the program about two years ago. I think the sequin format is nice if you want to have the features from Artemis in an excel table or print it. If you copy the sequin table to excel you get just that. Most people don't use the conversion program correctly because they don't enter EMBL. A common mistake is that there is no "FT" at the beginning of the lines with a feature table. I don't understand where people get this from since the feature tables come out of Artemis correctly. Since people don't use it too often I don't really get much feedback from it so it is hard for me to do any improvements. It is actually just a perl script that does the work. So if there is any interest, I could offer it for download, and people could run it on their own machines. Of course, the users would have to have the ability to run perl scripts. Greetings from germany, Michael. > Mike D-S > > > > Date: Mon, 23 Oct 2006 11:25:54 +0200 > > From: "Michael Nuhn" <[EMAIL PROTECTED]> > > Subject: Re: [Artemis-users] Preparing Artemis annotation for Sequin > > submission > > To: <artemis-users@sanger.ac.uk> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Re: [Artemis-users] Preparing Artemis annotation for Sequin > > submissionHello! > > > > I am the one who wrote the program that converts an embl file to > > sequin table format. > > > > If you have questions or need any assistance in using the program > > just ask me. > > > > You should definitely not do a copy and paste orgy. > > > > Regards from germany, > > Michael. > > > > ----- Original Message ----- > > From: Tim Carver > > To: Jay McCarren ; artemis-users@sanger.ac.uk > > Sent: Monday, October 23, 2006 10:31 AM > > Subject: Re: [Artemis-users] Preparing Artemis annotation for > > Sequin submission > > > > > > Hi Jay > > > > This web service may be of some use to you: > > > > http://nbc11.biologie.uni-kl.de/framed/left/menu/auto/right/ > > sequin/index_sequin.shtml > > > > ? > > > > Regards > > Tim Carver > > > > On 20/10/06 19:48, "Jay McCarren" <[EMAIL PROTECTED]> wrote: > > > > > > Hello, > > > > I'm in the process of submitting a number of fosmid sequences > > and associated annotation to Genbank using the NCBI Sequin > > submission software. I'm having difficulty porting my annotation > > into Sequin. So far I've only been partially successful by writing > > a file with the amino acids of all the CDSs and then importing this > > file in the Proteins tab during the sequin submission. This > > locates the CDS on my nucleotide sequence but I lose all the other > > important annotation. Is there a better way to go about this? Is > > there some way to generate a feature table? If so, how is this > > then imported in Sequin? It seems like there must be a more > > automated way about this than the cut and paste operation I'm about > > to embark on. > > > > Thanks for the help, > > Jay > > > > ______________________________ > > Jay McCarren > > Postdoctoral Associate > > Massachusetts Institute of Technology > > Room 48-336 > > 15 Vassar St. > > Cambridge, MA 02139 > > Lab: (617) 258-7407 > > Fax: (617) 253-7475 > > ____________________________ > Mike Dyall-Smith > Dept. Microbiology and Immunology > University of Melbourne > Ph: +61 3 8344 5693 > Fx: +61 3 9347 1540 > ____________________________ > > > > > _______________________________________________ > 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
