The first of several dermatophyte fungal genomes, [[Microsporum gypseum]], has been released at the Broad Dermatophyte site. Two Tricophyton species and another Microsporum genome should follow soon. These dermatophyte fungi are Onygenales (Ascomycota) fungi (like Coccidioides and Histoplasma).
Dermatophyte genome sequences
Posted on August 6th, 2008 by Jason Stajich · No Comments
Categories: coccidioides · onygenales
Tags: coccidioides, fungal, fungi, genome, genome sequence, microsporum, onygenales, release, sequence, sequences, sequencing, trichophyton
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
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
Podospora genome published
Posted on May 11th, 2008 by Jason Stajich · No Comments
The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings. The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons
Categories: comparative · genome · genome sequencing · neurospora · sordariomycetes
Tags: biology, comparative, coprophillic, dung, evolution, filamentous, fungi, fungus, genes, genome, neurospora, podospora, repeats, RIP, sequences, sequencing, species
Fungal Genetics 2007 details
Posted on March 28th, 2007 by Jason Stajich · 2 Comments
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences”.
Categories: Fungal Genetics · bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete
Tags: annotation, annotations, asilomar, aspergillus, basidiomycete, batrachochytrium, bioinforics, biology, candida, chytrid, clone, comparative, conferences & courses, coprinus, cryptococcus, definitions, development, diversity, ecology, endophyte, enzymes, evolution, experimental, frog, fungal, fungi, fungus, gene, genes, genome, genomes, horizontaltransfer, infection, JGI, maps, MAT, meetings, methods, microarray, microbes, multicellularity, mycological, neurospora, news, NRPS, organisms, pathogen, pathogens, phenotype, philosophy, phylogenetics, plant, plants, podospora, pombe, protein, repeats, rhizopus, RIP, s, saccharomyces, seminar, sequences, sequencing, SOLiD, speciation, species, strain, taxa, transcription, transcripts, wheat, yeast, zygomycete, zygomycetes
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
Tags: ajax, algorithm, annotations, bioinformatics, biology, experimental verification, external sources, genbank, genome annotation, genomes, holmes group, motivation, organisms, repository, sequences, steven salzberg, third party, tpa, wikis
Whole genome tiling arrays
Posted on February 1st, 2007 by Jason Stajich · No Comments
A recent paper describes the discovery of 9 new introns in Saccharomyces cerevisiae by Ron Davis’s group at Stanford, using high density tiling arrays from Affymetrix. The arrays are designed for both strands allow the detection of transcripts transcribed from both strands. The arrays were also put to work by the Davis and [...]
Categories: microarray · saccharomyces · tiling array · transcription
Tags: algorithm, annotation, annotations, cerevisiae, clone, cryptococcus, fungi, gene, genes, genome, genomes, hybrid, hybridization, intron, maps, microarray, news, parents, polymorphism, qtl, sequence, sequences, sequencing, species, tiling array, transcription, transcripts, yeast