On Fri, 29 Aug 2003 12:09:46 -0700, Philip Hugenholtz wrote: > Hi All > We've been annotating partial genome contigs in artemis and now have > those contigs assembled into one genome scaffold.
> Is there a simple way to change all of the ORF CDS coordinates in the > contigs at once to reflect the restructuring of the contigs into a > larger scaffold? (in artemis directly, or maybe a perlscript exists??) Hi. Artemis isn't able to re-map feature coordinates. This is quite a hard problem to solve because you need to deal with all the possible ways in which a contig can change between assembles. Potentially any insertion, deletion, split or join is possible. If you already know how the coordinates on the old contigs map to the new contigs, you should be able to update the coordinates with a bit of Perl. If not, you'll need to use a sequence comparison program (eg. Cross_match or BLASTN) to work out the mapping. The Ensembl project (http://www.ensembl.org/) does this for eukaryotic genomes using Cross_match (I believe) and the code is free. The down side is that Ensembl is a large package and so it may be overkill for your situation Kim.
