Re: [Artemis-users] Preparing Artemis annotation for Sequin submission

Mon, 23 Oct 2006 09:44:04 -0700

Hi, if you're annotating multiple sequences that are similar, you should look at our program:

Genome Annotation Transfer Utility (GATU) annotates a genome based on a very closely related reference genome. The proteins/mature peptides of the reference genome are BLASTed against the genome to be annotated in order to find the genes/mature peptides in the genome to be annotated.
Tcherepanov VT, Ehlers A, Upton C. (2006) Genome Annotation Transfer Utility (GATU): Rapid annotation of viral genomes using a closely related reference genome. 
BMC Genomics. 2006 Jun 13;7(1):150


It can take 90% of the drudgery out of annotation. And it writes a GenBank file at the end.

Cheers,
Chris



On Oct 23, 2006, at 1:31 AM, Tim Carver wrote:

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
 
______________________________


Chris Upton Ph.D.                                   Associate Professor

Biochemistry and Microbiology             Tel. 250-721-6507 

University of Victoria                                Fax  250-721-8855

P.O. Box 3055 STN CSC

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Canada  

                                                     

web.uvic.ca/~cupton

www.virology.ca

www.biodirectory.com/uptons_blog.html

  


 

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