CoGepedia:Current events

Linked to ProSite for protein domain searching

Dec. 24th 2009 FastaView is now linked to ProSite when viewing a protein sequence for protein domain searching. See this FastaView example and click on the link at the bottom of the page. Currently, we haven't figured out how to send more than one sequence to ProSite using CGI POST calls from javascript. Please e-mail us if you know how to work around this.

Improved implementation of DAGChainer in SynMap

Dec. 15th 2009

Thanks again to Brent Pedersen for some fantastic programming. He discovered that DAGChainer's C++ code's makefile did not include the -O3 optimization, rewrote the input/output methods of the compiled binary to read from STDIN instead of a file, and rewrote the perl front-end in python. Together, these changes increase CoGe's DAGChainer implementation in SynMap between 2-4 fold.

You can download his code at: svn co http://bpbio.googlecode.com/svn/trunk/scripts/dagchainer

CoGe Workshop being taught at SIP 2010

Nov. 30th 2009

Genomics: What every invertebrate pathologist needs to know. http://www.sip2010.org/index.php/Bioinformatics-Workshop.html

CoGe on OpenHelix and James and the Giant Corn

Nov. 18th 2009

Phillipe Lamesch from TAIR passed along a link to openhelix.com highlighting CoGe's tool GEvo. They put together a nice video showing GEvo. They, in turn, found this on a posting at the blog of James and the Giant Corn who had used GEvo for a grant proposal.

Maize Pseudomolecule Assembly with Gene Models Released

Oct. 20th 2009

Thanks to maizesequence.org for providing the sequence and annotations. The current pseudomolecule assembly of maize has been loaded into CoGe.

• Link to OrganismView for complete set of gene models.
• Link to OrganismView for filtered gene model set.
• Maize-Sorghum syntenic dotplot with syntologs colored by synonymous rate change.
• Maize-Maize syntenic dotplot with syntologs colored by synoonymous rate change.

CoGe surpasses 7000 organisms in its database!

More fun for everyone!

NCBI Genome Loader Updated

CoGe's automated NCBI genome loader has been updated and is once again checking NCBI regularly for new and updated genomes. You can get a snapshot of the number or organisms and genomic sequence in CoGe by checking its homepage, search for your genome of interest using OrganismView.

CoGe is linked to TARGeT: Tree Analysis of Related Genes and Transposons

You can send a set of fasta sequence generated by FastaView directly to TARGeT.

New version of Gobe release!

Read general announcement Gobe

Version 3 of CoGe is released!

Read general announcement CoGe version 3.