A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the annotation team at Broad’s gene calling pipeline.
Updated Cryptococcus serotype A annotation
Posted on December 9th, 2008 by Jason Stajich · 1 Comment
Categories: cryptococcus · genome · genome annotation · genome sequencing · human pathogen
Tags: animal pathogen, annotation, broad institute, cryptococcus, database, human pathogen, news, update
Fungal P450s
Posted on October 5th, 2008 by Jason Stajich · No Comments
A paper (Park et al, BMC Genomics) from Fungal Bioinformatics Lab at Seoul University in South Korea describes their new “Fungal P450 Database”. The database contains sequence, names, and genome links for P450’s (or Cytochrome P450s) identified by similarity and phylogenetic classification from genome annotations.
Categories: P450 · ascomycota · basidiomycota
Tags: basidiomycete, comparison, database, filamentous fungi, functional annotation, genome, nomenclature, P450, phylogenetic, phylogenomics, species comparisons
A word about databases
Posted on July 27th, 2008 by Jason Stajich · 1 Comment
Report concludes that a fungal genome database is of “the highest priority”.
This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.
Categories: opinion
Tags: bioinformatics, bioinformatics support, comparative, curation, database, funding, fungal, fungal genome database, fungi, gene, genes, genome, genomes, gmod, maps, news, pathogen, pathogens, protein, pubmed, reporting, reports, research, sequences, sequencing, species, strain, systematics, transcription, transcripts
AAM Releases “The Fungal Kingdom” Report
Posted on July 9th, 2008 by Jason Stajich · 2 Comments
The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research.
Categories: news · science policy
Tags: American Society for Microbiology, annotation, ASM, database, functional, fungal, genomes, news, reporting, reports, research, sequencing
Trichoderma reesei genome paper published
Posted on May 12th, 2008 by Jason Stajich · 1 Comment
The [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.
Categories: filamentous · gene family · genome · genome annotation · genome sequencing · trichoderma
Tags: aspergillus, biofuel, cellulase, comparative, database, definitions, enzymes, evolution, fermentation, filamentous, fungi, fungus, fusarium, genome, genomes, JGI, magnaporthe, pathogens, phylogenetics, s, sequences, sequencing, species, systematics, trichoderma
(re)Annotating GenBank
Posted on March 22nd, 2008 by Jason Stajich · No Comments
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 traces.
Categories: database · fungi · metagenomics · news
Tags: alignment, database, definitions, experimental, fungi, gene, genes, genome, metagenomics, news, phylogenetics, sequencing, wiki
Some links
Posted on March 3rd, 2008 by Jason Stajich · 2 Comments
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.
Categories: basidiomycota · database · extremophiles · molecular evolution · pathogens · zygomycete
Tags: ancestor, ancestral, brown rot, comparative, cryptococcus, database, enzymes, evolution, extremophiles, functional, fungi, fungus, genome, lignin, news, oxidoreductases, phylogenetics, reconstruction, rhizopus, taxa, toxin, white rot, yeast
Swissprot/UniProt curating fungal proteins
Posted on February 11th, 2008 by Jason Stajich · No Comments

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 05-Feb-2008
Categories: bioinformatics · database · fungi · genome · genome annotation · genome sequencing · news
Tags: curation, database, fungal genes, genome, protein, swissprot, uniprot
Linkathon
Posted on November 13th, 2007 by Jason Stajich · 1 Comment
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 [...]
Categories: bioinformatics · comparative · database · fungi · genome · phylogenetics
Tags: coprinus, corn smut, database, fungi, mushroom, orthogroups, pathogen, synergy, systematics, ustilago maydis
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
Tags: database, genome annotation, saccharomyces, wiki
