Take a look at this post by Larry Moran on Takao Kasuga’s paper on phylogenetic distribution of genes in N. crassa genome.
N.crassa lineage specific genes
Posted on April 22nd, 2009 by Jason Stajich · No Comments
Categories: evolution · genome annotation · neurospora · phylogenomics
Tags: annotation, neurospora, phylogenomics
Coprinopsis cinereus genome annotation updated
Posted on January 21st, 2009 by Jason Stajich · No Comments
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 [...]
Categories: Agaricomycota · basidiomycota · database · genome annotation · genome sequencing
Tags: annotation, broad, coprinopsis, coprinus, genome, kinome, meiosis, sequence release
Updated Cryptococcus serotype A annotation
Posted on December 9th, 2008 by Jason Stajich · 1 Comment
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.
Categories: cryptococcus · genome · genome annotation · genome sequencing · human pathogen
Tags: animal pathogen, annotation, broad institute, cryptococcus, database, human pathogen, news, update
Gene prediction without training?
Posted on September 7th, 2008 by Jason Stajich · No Comments
A new paper in Genome Research from Borodovsky lab at Georgia Tech provides an improved ab initio gene prediction building on their previous program GeneMark called GeneMark.hmm ES. This application doesn’t require a training set when building models for gene prediction in fungal genomes and reports to have as good or better sensitivity and specificity than most of the commonly used ab initio programs.
Categories: bioinformatics · fungi · genome annotation · mRNA splicing
Tags: annotation, fungi, gene prediction
Cochliobolus genome released
Posted on July 17th, 2008 by Jason Stajich · 1 Comment
Just noticed that the [[JGI]] has released the Cochliobolus heterostrophus genome sequence at their site predicting 9,633 protein-coding genes. Torrey Mesa Research Institute had access to a sequence many years ago, but it isn’t until now that public version of this genome is available. Cochliobolus is has been a model plant pathogen system and its production of T-Toxin by a PKS gene (Yang et al)
Categories: pezizomycota
Tags: annotation, cochliobolus, fungi, genome, genomes, infection, JGI, pathogen, pathogens, PKS
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
Basidiomycete genomes galore
Posted on June 1st, 2008 by Jason Stajich · Comments Off
Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles. I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics. I’m happy I got a chance to meet more folks in the community and learned about where informatics is needed
Categories: conferences & courses
Tags: annotation, annotations, basidiomycete, biology, conferences & courses, curation, development, gene, genome, genomes, meetings, sequencing, species
Lest you think annotation is easy
Posted on April 12th, 2008 by Jason Stajich · No Comments
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 works
Categories: bioinformatics · comparative · database · genome
Tags: annotation, ensembl, gene structure, genome, genome browser, genome centers, genome comparisons, management issues, prediction programs
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
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
