MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'annotation'. Sat, 03 Sep 2011 02:27:20 +0100 http://www.medworm.com/index.php?rid=4560491&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F1ryY5ataWZ8%2F As an update to previous post, the N. crassa annotation has been updated to version 5 on the Broad Institute website. Previously the data was not yet available for this update, but as of 8-Mar-2011 it is.  The assembly hasn’t changed but the annotation is updated and includes some fixes to improperly renamed locus names.  On the N. crassa genome site you can see files with the history of loci through this to determine if a locus name was improperly changed in the past. This should be rectified in the currently released annotation, and definitely encourage you to take it for a spin and report back to the Broad Institute if you have any questions. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4560491 Tue, 08 Mar 2011 22:43:27 +0100 4560491 http://www.medworm.com/index.php?rid=4477979&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FG1cDclcbn9Q%2F Here is a message from the Broad Institute about a gene annotation update that was made recently in response to an issue that was revealed in the June 2010 release.  This new version is called V5 and should be on its way to GenBank. Dear Neurospora scientists, Recently we discovered an issue with the way locus tags were assigned to our most recent Neurospora gene set, released publicly on the Broad website in June of 2010. Many genes in this gene set have mismatched locus numbers compared to the same genes released in February 2010. Adding to the confusion, both releases were labeled version 4. To remedy this we have recalled the June locus numbers and released a new, version 5 gene set. Genes in this set have been numbered to preserve historical locus numbers (back to the original gen... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4477979 Mon, 14 Feb 2011 23:36:32 +0100 4477979 http://www.medworm.com/index.php?rid=4285301&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrYtx4OOtgDY%2F Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy. These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). Wh... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4285301 Thu, 23 Dec 2010 16:11:50 +0100 4285301 http://www.medworm.com/index.php?rid=3790742&cid=t_95543_107_f&fid=35026&url=http%3A%2F%2Fhomepage.mac.com%2Fjonathan_eisen%2FPDFs%2F5.Eisen.SNF2.1995.pdf Just got an announcement regarding this challenge: Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations | Automated Function Prediction 2011 July 15-16 2011, Vienna, Austria Here is a description: CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will t... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3790742 Mon, 26 Jul 2010 23:08:52 +0100 3790742 http://www.medworm.com/index.php?rid=3743644&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FqAGH5CCKq5k%2F I am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers.  The data and analyses from these efforts are presented in a publication appearing in Nature Biotechnology today. Studies in mushrooms can have important impact on other research areas.  They can be useful in biotechnology as protein biosynthesis factories for producing compounds or even as an edible delivery mechanism for new drugs.  What we found in the analysis of this genome include clues to mechanisms of how white rotting fungi degrade lignin through analysis of enzyme families.  We also ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3743644 Mon, 12 Jul 2010 07:12:10 +0100 3743644 http://www.medworm.com/index.php?rid=3710720&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FHmUqNNb51wE%2F I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus.  You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper. Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D.,... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3710720 Tue, 29 Jun 2010 17:35:11 +0100 3710720 http://www.medworm.com/index.php?rid=3208533&cid=t_95543_122_f&fid=36582&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FSharpBrains%2F%7E3%2FuP6E-oQhJ1Q%2F Rumor has it that Apple is going to announce a tablet computer, which may well become a revolutionary new way for users to read and experience all kinds of educational content. Will it support or hinder our Cognitive  Fitness? In this article, I describe the criteria that a tablet computer—and its technological ecosystem—must meet in order for the solution to make users more knowledgeable and smarter. To achieve these lofty goals, the tablet must be much more than an “e-reader”. The offering must be an integrated learning environment with which users transform the information that they read, hear and view on the tablet into their own knowledge. The key consideration in designing such a system is that productive reading is active reading. In other words, learning involves a lot of ... SharpBrains blogs http://www.medworm.com/rss/comments.php?id=3208533 Tue, 26 Jan 2010 15:20:13 +0100 3208533 http://www.medworm.com/index.php?rid=2358018&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FcxMadoakYds%2F Have a look at this post by Larry Moran on Takao Kasuga’s PLoS One paper on phylogenetic distribution of genes in N. crassa genome. The interesting next step with this paper, some of which we’re exploring as part of the Neuropsora tetrasperma and N.discreta genome sequencing, is how many of these N.crassa genes are at least shared with other Neurospora spp and whether they show a nucleotide conservation pattern that suggests they are protein coding genes. We also haves some RNASeq and microarray gene expression data to test if these species-specific genes are expressed any under conditions. So far there isn’t much evidence to throw out many of the 10k or so genes as artifacts, but the analysis is still a work in progress. Figure 1. Lineage specificity classification of ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2358018 Wed, 22 Apr 2009 22:11:38 +0100 2358018 http://www.medworm.com/index.php?rid=2274488&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FvBv9bKMjBKQ%2F In preparation for Asilomar, JGI is releasing lots of the genome sequencing project portals. The Schizophyllum commune Genome Portal is now publicly available. Go get your white-rot gene investigation on! (Though please respect the community rules for 1st rights to publication of the genome-wide analyses). © Jason Stajich for The Hyphal Tip, 2009. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Agaricomycota, genome, genome annotation, genome sequencing. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2274488 Mon, 16 Mar 2009 22:55:14 +0100 2274488 http://www.medworm.com/index.php?rid=2271656&cid=t_95543_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F03%2Freflect-annotate-protein-and-small.html The core component of Reflect is a consolidated dictionary that links names and synonyms to source data entries. It was created by merging the STRING and STITCH databases, and it currently contains over 1.5 million proteins from 373 organisms and 4.3 million small molecules..The Reflect site annotates any web page provided, or installs a FireFox plug-in to allow annotation of any web page after a right mouse-click 'reflect this page'. Here an example for the tumor protein p53.The reflect team of Reinhard Schneider is one of the Elsevier grand challenge finalists (sorry, for making the wrong statement before that they won this challenge, which is not known, yet). (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2271656 Mon, 16 Mar 2009 18:50:00 +0100 2271656 http://www.medworm.com/index.php?rid=2227456&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrldRjqU82Kw%2F I have cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences.   The group had previously submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published…  The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus. This paper addressed several challenges including methodology for light genome sequencing for population genomics. This data represents in a way, a pilot project on for genome reseq... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2227456 Sun, 01 Mar 2009 10:00:06 +0100 2227456 http://www.medworm.com/index.php?rid=2177560&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2009%2F02%2Fntetrasperma-ndiscreta%2F 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 highly colinear with the N.crassa genome.  With the JGI, we’ve also done some additional 454 sequencing which will represent an improved assembly and 23X coverage in the next release.  We also did some comparative scaffolding and can basically double that N50 - most of which looks good when compared to the improved V2 assembly. The N.discreta assembly (8X) is also quite good with an N50 of 2.3 Mb. For comparison, the V7 of N.crassa has an N50 ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2177560 Wed, 11 Feb 2009 07:08:50 +0100 2177560 http://www.medworm.com/index.php?rid=2167712&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FCAIJslFGq0M%2F Postia placenta genome is now published in early edition of PNAS.   Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters break down cellulose but cannot break down lignin or lignocellulose while white rotters (like the previously sequenced Phanerochaete chrysosporium) are able to break down the lignin.  This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author - go Diego!). It is also helpful to contrast the white and brown rotters t... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2167712 Fri, 06 Feb 2009 07:29:42 +0100 2167712 http://www.medworm.com/index.php?rid=2147612&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F527593699%2F 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 are available from the FGSC. We’re also integrating SNP data using the HapMap glyphs in which you can see one way to view this information in the Genome Browser for Coccidioides.  Working on other information including PhastCons conservation profiles and other information in our development server and hope to make this public soon. © Jason Stajich for The Hyphal Tip, 2009. | Permalink | No comment Add to del.icio.us Search blogs linking... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2147612 Fri, 30 Jan 2009 22:12:54 +0100 2147612 http://www.medworm.com/index.php?rid=2121796&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F519249058%2F 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 the globe including a BAC map from H. Muraguchi.  Thanks to Jonathan Goldberg and colleagues at the Broad Institute for getting this updated annotation out the door.   This updated annotation is able to join and split several sets of genes and the gene count sits at just under 14k genes in this 36Mb genome. There are a couple of hiccups in the GTF and Genome contig/supercontig file naming that I am told will be fixed by early next ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2121796 Thu, 22 Jan 2009 00:42:40 +0100 2121796 http://www.medworm.com/index.php?rid=2027166&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F479999669%2F 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 genome annotation team at the Broad Institute. Some changes noted by the Broad Institute include: “This release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a new genomic assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. The new assembly consists of 14 nuclear chromosomes and a single 21 KB mitochondrial chromosome, and has resulted in a reduction of the estimated genome size from 19.5 to 18.9 Mb. Improvements in the assembly and in our annotation process h... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2027166 Tue, 09 Dec 2008 23:18:06 +0100 2027166 http://www.medworm.com/index.php?rid=1926551&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F438436400%2F Genome Technology highlights the very cool thing about next-gen sequencing - it puts the power in the hands of the researchers to explore genome sequence and doesn't limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke's Institute for Genome Sciences and Policy through their next-gen sequencing program. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues. This isn't the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has take... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1926551 Fri, 31 Oct 2008 20:56:54 +0100 1926551 http://www.medworm.com/index.php?rid=1853649&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F412456461%2F 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.  The group is using most of annotated genomes in GenBank (and I think some from elsewhere) of bacterial, fungi, animals, and plants. I find the current nomenclature for this family of genes confusing but it has been I am sure a difficult job and wrangled to a large part by David Nelson (who also has a new paper on the CYPome of Aspergillus nidulans). I have found it difficult to follow the logic for naming these members, as it didn't seem to be particularly phylogenetic a... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1853649 Mon, 06 Oct 2008 04:43:33 +0100 1853649 http://www.medworm.com/index.php?rid=1773246&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F386008719%2F 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. They are picking up on proviously described insights about fungal gene structures and introns which is the lack of a necessary branch site and varying degrees of conservation of splice-sites in most intron rich fungi (Schwartz et al, 2008) and that these intron sizes remain short across the fungi (Stajich et al. 2007). In practice it should simplify the initial genome annotation protocols ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1773246 Sun, 07 Sep 2008 20:02:16 +0100 1773246 http://www.medworm.com/index.php?rid=1634966&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F338156072%2F 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). © Jason Stajich for The Hyphal Tip: Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under pezizomycota. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1634966 Thu, 17 Jul 2008 15:49:31 +0100 1634966 http://www.medworm.com/index.php?rid=1603096&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F331008458%2F 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. One recommendation that makes the top of the list is an integrated database for fungal genomes, something we're keenly interested in seeing happen.  This sort of centralized repository of functional annotation, literature links, and genome sequences and annotation is critical given the 150+ genomes that are available or on their way.  Systematic re-annotation with consistent tools, comparative analyses and gene predictions, and linking gene sequences by homology and ortholog predictions are a critical component to fully utilizing the genomic data that has been produced for the fungi ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1603096 Wed, 09 Jul 2008 18:49:15 +0100 1603096 http://www.medworm.com/index.php?rid=1484935&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F302439648%2F 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 and computational approaches are really needed to push along some of the interpretation of the more than a dozen basidiomycete genomes.  In particular it sounds like the Pleurotus, Schizophyllum, Agaricus bisporus, and Serpula genomes are all marching along to completion with some already in 4X assembly or further.   So we'll further have more samples from... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1484935 Sun, 01 Jun 2008 17:04:19 +0100 1484935 http://www.medworm.com/index.php?rid=1469733&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F298471576%2F This month's Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae Chlamydomonas reinhardtii. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include: Exploration of snoRNAs finding that a large fraction are clustered in the genome and located in introns. Description of transcription factors and their evolutionary conservation and potential link to multicellularity. Duplication and diversification of the RNA processing machinery for small RNA mediated silencing. Gleaning additional information from Chlamy ESTs that have been over-trimmed. Integrating metabolomics and proteomics into better genome annotation. Evolution of s... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1469733 Tue, 27 May 2008 00:25:59 +0100 1469733 http://www.medworm.com/index.php?rid=1436934&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F288882594%2F 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 or other biofuels production.  The fungus also has starring roles in industrial processes like making stonewashed jeans due to its prodigious cellulase production. The most surprising findings from the paper include the fact that there are so few members of some of the enzyme families even though this fungus is able to generate enzymes with so much cellulase activity. The authors found that there is not a significantly larger numb... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1436934 Mon, 12 May 2008 19:27:46 +0100 1436934 http://www.medworm.com/index.php?rid=1368869&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F269197633%2F 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 ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1368869 Sun, 13 Apr 2008 03:00:48 +0100 1368869 http://www.medworm.com/index.php?rid=1223724&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F233360453%2F 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. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under bioinformatics, database, fungi, genome, genome annotation, genome sequencing, news. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1223724 Mon, 11 Feb 2008 22:42:37 +0100 1223724 http://www.medworm.com/index.php?rid=931165&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F165833488%2F Few 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. The authors point out several interesting things about these genes of unknown functi... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=931165 Fri, 05 Oct 2007 20:47:03 +0100 931165 http://www.medworm.com/index.php?rid=873756&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F09%2Ffusarium-graminearum-genome-published%2F The genome of the wheat and cereal pathogen Fusarium graminearum was published in Science this week in an article entitled "The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specializationtion". The project was a collaboration of many different Fusarium research groups. The genome sequencing was spearheaded by the Broad Institute at Harvard and MIT and is part of a larger project to sequence several different species of Fusarium. The group sequenced a second strain in order to identify polymorphisms. Some of the key findings The presence of Repeat Induced point-mutation (RIP) has likely limited the amount of repetitive and duplicated sequences in the genome Most of the genes unique to F. graminearum (and thus not present in 4 other Fusarium spp gen... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=873756 Wed, 12 Sep 2007 06:16:39 +0100 873756 http://www.medworm.com/index.php?rid=814239&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F146674653%2F Not sure when this went live but the Postia placenta annotation is available on the JGI site. 17k genes are predicted which is in the neighborhood of Laccaria. genome, genome annotation (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=814239 Tue, 21 Aug 2007 22:10:45 +0100 814239 http://www.medworm.com/index.php?rid=623644&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F118102957%2F From Genetics this week a review discusses Why are there still 1000 Uncharacterized Yeast genes? Poor Yeast - so many more genes have no known function, while S. pombe has nearly 100% coverage in functional annotation. I’ll also point out that the 1000 genes refers to protein-coding genes, not ncRNA genes which may mean that there is alot more that is unknown. I think this sentence from the abstract hits the nail on the head. Notably,the uncharacterized gene set is highly enriched for genes whose only homologs are in other fungi. Achieving a full catalog of yeast gene functions may require a greater focus on the life of yeast outside the laboratory. (more…) gene function, genome annotation, saccharomyces, yeast © Jason Stajich for Fungal Genomes and Comparative Genomi... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=623644 Sun, 20 May 2007 05:18:04 +0100 623644 http://www.medworm.com/index.php?rid=554679&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F04%2Forthology-detection-software%2F 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 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 comb... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=554679 Thu, 19 Apr 2007 17:56:00 +0100 554679 http://www.medworm.com/index.php?rid=519343&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F04%2Fthat-was-a-lot-of-work%2F I’ve never worked with Magnaporthe grisea, the fungus responsible for rice blast, one of the most devastating crop diseases, but I do know that its life cycle is complicated and that knocking out roughly 61% of the genes in the genome and evaluating the mutant phenotype to infer gene function is not trivial. In their recent letter to Nature, Jeon et al did what many of us have dreamed of doing in our fungus of interest: manipulate every gene to find those that contribute to a phenotype of interest. In their study, the authors looked for pathogenecity genes. Interestingly, the defects in appressorium formation and condiation had the strongest correlation with defects pathogenicity, suggesting that these two developmental stages are crucial for virulence. Ultimately, the authors identi... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=519343 Tue, 03 Apr 2007 17:20:14 +0100 519343 http://www.medworm.com/index.php?rid=486601&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F03%2Fsgd-community-annotation%2F 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. database, genome annotation, saccharomyces, wiki © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under saccharomyces, database, genome annotation, wiki. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486601 Wed, 14 Mar 2007 01:00:11 +0100 486601 http://www.medworm.com/index.php?rid=486603&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F03%2Fapproaching-100-coverage-for-go-assignments-in-spombe%2F A paper by Martin Aslett and Val Wood indicate that the fission yeast community is approaching 100% coverage of a GO annotation for every gene in the S. pombe genome. Only Ashbya gossypii has a smaller genome in the fungi (see a recent paper on Ashbya annotation database) and doesn’t yet have complete GO coverage. This is quite remarkable and a great dataset for studies in S. pombe and all fungi. My quick predictions of genes a closely related species, S. japonicus, has more than twice as many genes as S. pombe. Taken in comparison to many other fungi, S. pombe represents a streamlined and reduced genome which probably occured indepdently from reduction in the Hemiascomycetes. functional, genome annotation © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486603 Mon, 05 Mar 2007 02:41:23 +0100 486603 http://www.medworm.com/index.php?rid=486608&cid=t_95543_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F02%2Fwikis-for-genome-reannotation%2F 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. (more…) bioinformatics, genome annotation © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | 5 comments Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under genome annotation, bioinformatics. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486608 Mon, 12 Feb 2007 07:45:34 +0100 486608