Difference between revisions of "CoGepedia:Current events"

Revision as of 19:29, 16 February 2010

New plant genomes in CoGe

Feb. 10th 2010

Mimulus guttatus (monkey flower): http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=30760 Mimulus is an outgroup to the rosids (in the sister group, the asterids)

Populus trichocarpa (Poplar; cotton wood): http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=324 Version 2 of poplar!

Both are from the JGI.

MaizeGDB links to GenomeView

Feb. 8th 2010 MaizeGDB is now linking to CoGe's GenomeView so maize researchers can find maize-sorghum syntenic gene sets and quickly perform syntenic analyses using GEvo. For an example view from MaizeGDB's genome broswer:

http://gbrowse.maizegdb.org/cgi-bin/gbrowse/maize/?name=chr1:1000000..1200000

For instructions on how to perform this workflow: MaizeGDB and CoGe

For more information on maize-sorghum syntenic analyses: Maize-Sorghum genome analyses

For a quick video walk through of the new connections: MaizeGDB_and_CoGe.27s_Maize-Sorghum_Orthologies

Syntelog visualization in GenomeView

Feb. 5th 2010 GenomeView has been updated to auto-detect genomic features with annotations that are links to GEvo. These links provide an analysis of a genomic feature (e.g. gene) to previously identified syntologous sets of features. Currently, this has been implemented using syntelogs from maize and sorghum, but with the code in place, we will expand annotations for genomic features from other organisms for which we generated syntologous gene sets. For an example of this visualization in GenomeView please see: | this GenomeView of sorghum. Also, for an expanded list of glyphs used in GenomeView please refer to these examples.

Easy exporting and downloading of genomes

Jan. 16th 2010 OrganismView has new options for easily downloading the sequences of a genome in fasta format and retrieving all of its annotations in an GFF file. To access, just search for an organism and genome of interest, and look for the links under "Genome Information".

FastaView is linked to phylogeny.fr for one-click phylogenetics

Jan. 10th. 2010

We've linked to phylogeny.fr for quick and easy phylogenentic tree reconstruction. Now, you can build a list of fasta sequences and display them in FastaView, select protein or DNA sequences, edit them if necessary (e.g. add or remove sequences manually), and press a button to send them off to phylogeny.fr for:

1. multiple sequence alignment (MUSCLE)
2. maximum likelihood phylogenetic tree reconstruction (PhyML)
3. tree visualization (TreeDyn)

For an example, use this link to FastaView and press the button "phylogeny.fr" at the bottom of the screen.

Special thanks to Haibao Tang for pointing out this incredible web resource!

Haibao Tang joins the Freeling lab

Jan. 4th 2010

Haibao Tang, an expert in plant comparative genomics and genome evolution, as well as a great python programmer, has joined the Freeling lab. His input and contributions will be most valued!

New tutorials added

Jan. 4th 2010

New tutorials have been added:

• How to find syntenic regions between genomes
• How to find inversions
• How to find rarely and frequently used codons in a genome
• How to generate an amino acid usage table for a genome
• Using synonymous mutation rates in SynMap to rapidly identify different whole genome evolutionary events
• How to extract all gene sequences from a genomic region
• How to identify putative horizontal gene transfer 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.

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. Major feature: transparent wedges are drawn to connect regions of sequence similarity.

Version 3 of CoGe is released!

Read general announcement CoGe version 3.