By Jason Stajich, on March 12th, 2009
Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. In homage to his earlier street art we’ll discuss the growing Aspergillus genome [...]
By Jason Stajich, on February 9th, 2009
The JGI in collaboration with our lab at Berkeley have released the Neurospora tetrasperma (mat A) and N. discreta (mat A) genome sequences and annotation after about two years of work. These are two closely related species to the well studied laboratory workhorse Neurospora crassa.
The N.tetrasperma assembly (8X) has an N50 of 976kb and is [...]
By Jason Stajich, on January 30th, 2009
I’m working to make more data available in the genome browsers for fungi. One is adding in the Primer information from the Neurospora KO project to the Neurospora browser to indicate the position and primer sequences for all the gene knockouts being (or already) constructed. At least 60% of the genes have been knocked out and [...]
By Jason Stajich, on January 21st, 2009
The Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across [...]
By Jason Stajich, on April 12th, 2008
Ewan Birney and Ensembl (the other/original genome browser depending on if you are a UCSC junkie) have started blogging a bit more about what is going on under the proverbial hood over there in Hinxton. There are some great nuggets talking about what are some of the current problems. These bite-sized comments should be a great glimpse into how Ensembl [...]
By Jason Stajich, on March 22nd, 2008
Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition. This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species.
There’s a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I’m sure he is thinking of many examples, like reclassifying some Drosophila sequence [...]
By Jason Stajich, on March 3rd, 2008

I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.
By Jason Stajich, on February 11th, 2008

The UniProtKB/Swiss-Prot team is curating fungal proteins in their databases and reportedly have curated more than 20,000 fungal proteins in Release 54.8 of [...]
By Jason Stajich, on November 13th, 2007
Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I’ve been remiss in reviewing the paper myself, but they’ve created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there [...]
By Jason Stajich, on March 13th, 2007
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 [...]