Category Archives: bioinformatics

Lest you think annotation is easy

Ensembl!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 what is going on without drowning in the deluge that is ensembl-dev.  

This is a recent post on the challenges of gene annotation coordination among “manual” and “automated” annotation of gene structure of groups at the same institution.  

Scale that up among multiple genomes, genome centers, quality of prediction programs and assemblies, and you can see why the fungal genome comparisons could use a little bit more help. It is great to hear what the animal genome annotation groups are doing to solve informatics challenges and data management issues and coordination. I’m big fan of more informatics+science in the open where it is feasible. 

Sex in fungi: MAT locus cloned from a Zygomycete

On the cover of this week’s Nature is a picture of Phycomyces blakesleeanus Nature Coverhighlighting the discovery of the MAT locus in this Zygomycete fungus from Alex Idnurm and Joe Heitman and colleagues. While it was previously known that Zygomycetes (the Orange lineage represented by R. oryzae in the tree below) mate, the specific locus has until now, never been discovered. The authors in this study identified the MAT locus through a sequence search looking for HMG-box genes knowing that these are found the Mating Type locus in Basidiomycetes and Ascomycetes. They confirmed the identity through a through set of experiments that included PCR, sequencing and crosses of (+) and (-) strains of P. blakesleeanus, and Southern blots.

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Saccharomyces strain sequencing

Blogging on Peer-Reviewed ResearchWhile many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled “Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789”.

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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 is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. corn smut

The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut.

Chris and Tom took some more Coprinus pictures while I was away from the lab.

Yes, Ecology can improve Genomics

Blogging on Peer-Reviewed ResearchFew 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. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.

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Evolution of aflatoxin gene cluster

Blogging on Peer-Reviewed ResearchIgnazio Carbone and colleagues published a recent analysis of the evolution of the aflatoxin gene cluster in five Aspergillus fungi entitled “Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster” in BMC Evolutionary Biology. The authors were able to identify seven modules pairs of genes whose history of duplication were highly correlated. Several genomes of Aspergillus have been sequenced along with more Eurotioales fungi. Continue reading Evolution of aflatoxin gene cluster

Orthology detection software

Blogging about Peer-Reviewed Research 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. The authors discuss the trade-offs between highly sensitive specific tree-based methods and fast but less sensitive approaches of the Best-Reciprocal-Hits from BLAST or FASTA or some of the hybrid approaches. The authors employ Latent Class Analysis (LCA) to aid in “evaluation and optimization of a comprehensive set of orthology detection methods, providing a guide for selecting methods and appropriate parameters”. LCA is also the statistical basis for feature choice in combing gene predictions into a single set of gene calls in GLEAN written by many of the same authors including Aaron Mackey.

I’ve been reading a lot of orthology and gene tree-species tree reconcilation papers lately, some are listed in Ian Holmes’s group as well as listing some of the software on the BioPerl site. This also follows with on our Phyloinformatics hackathon work which we are trying to formalize in some more documentation for phyloinformatics pipelines to support some of the described use cases. I’m also applying some of this to a tutorial I’m teaching at ISMB2007 this summer.

Fungal Genetics 2007 details

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 we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

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Wikis for genome (re)annotation

Steven Salzberg (who is nominated for the Franklin award at has an opinion piece in Genome Biology proposing wiki technology to help solve the problem of genome annotations getting out of date.
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