Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
Yes, Ecology can improve Genomics
Posted on October 5th, 2007 by sharpton · 1 Comment
Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast
Fusarium graminearum genome published
Posted on September 8th, 2007 by Jason Stajich · 1 Comment
The genome of the wheat and cereal pathogen Fusarium graminearum was published in Science this week in an article entitled "The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specializationtion". The project was a collaboration of many different Fusarium research groups.
Categories: RIP · filamentous · fusarium · genome · genome annotation · genome sequencing · plant pathogen
Postia annotation
Posted on August 21st, 2007 by Jason Stajich · No Comments
Not sure when this went live but the Postia placenta annotation is available on the JGI site. 17k genes are predicted which is in the neighborhood of Laccaria.
Categories: genome · genome annotation
Yeast genome: Known knowns, and known unknowns
Posted on May 20th, 2007 by Jason Stajich · 1 Comment
From Genetics this week a review discusses Why are there still 1000 Uncharacterized Yeast genes? Poor Yeast - so many more genes have no known function, while S. pombe has nearly 100% coverage in functional annotation. I'll also point out that the 1000 genes refers to protein-coding genes, not ncRNA genes which may mean that there is alot more that is unknown.
Categories: gene function · genome annotation · saccharomyces · yeast
Orthology detection software
Posted on April 19th, 2007 by Jason Stajich · 1 Comment
A paper in PLoS One, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, reports a new approach to assess the performance of automated orthology detection. These authors also wrote the OrthoMCL (2006 DB paper, 2003 algorithm paper) which uses MCL to build orthologous gene families.
Categories: bioinformatics · comparative · genome annotation · methods
That was a lot of work
Posted on April 3rd, 2007 by sharpton · No Comments
I've never worked with Magnaporthe grisea, the fungus responsible for rice blast, one of the most devastating crop diseases, but I do know that its life cycle is complicated and that knocking out roughly 61% of the genes in the genome and evaluating the mutant phenotype to infer gene function is not trivial. In their recent letter to Nature, Jeon et al did what many
Categories: functional · fungi · gene function · genome · genome annotation · magnaporthe · plant pathogen
SGD community annotation
Posted on March 13th, 2007 by Jason Stajich · No Comments
The Saccharomyces Genome Database has deployed a wiki for gene annotation from the community. This should be an interesting experiment in how information can flow from the community into these databases.
Categories: database · genome annotation · saccharomyces · wiki
Approaching 100% coverage for GO assignments in S.pombe
Posted on March 4th, 2007 by Jason Stajich · 2 Comments
A paper by Martin Aslett and Val Wood indicate that the fission yeast community is approaching 100% coverage of a GO annotation for every gene in the S. pombe genome. Only Ashbya gossypii has a smaller genome in the fungi (see a recent paper
Categories: functional · genome annotation · s.pombe
Wikis for genome (re)annotation
Posted on February 12th, 2007 by Jason Stajich · 5 Comments
Steven Salzberg (who is nominated for the Franklin award at bioinformatics.org) has an opinion piece in Genome Biology proposing wiki technology to help solve the problem of genome annotations getting out of date.
The problem comes down to how annotations are banked. Some people regard GenBank as the gold standard master for annotations, but it only provides a bank.
Categories: bioinformatics · database · genome annotation · wiki