I was catching up on some mailing list reading last week when I saw an unusual item come across the UCSC discussion mailing list. Someone who is in the process of obtaining genome and transcriptome sequence for a new project asked the UCSC group for guidance on what to do with it. It’s actually a [...]
Being summer, a strangely slow connection and some other factors, I am embedding a talk from Doug Ramsey (posted on SciVee) on the GEBA project at JGI (instead of doing a tip myself . The GEBA project recognizes that many, if not most, of the bacterial and archaeal genomes that have been sequenced to date [...]
In the continuing effort to get scientists and researchers to annotate and curate data and to capture the huge amount of knowledge available, UCSC Genome Browser has added a wiki annotation track to the browser. It’s not the first effort of course, GeneWiki is an effort, with mixed results so far, to annotate gene function [...]
In the push to ‘communitize’ annotation and curation, one journal, RNA Biology, is requiring submitters to add or update their RNA sequences on wikipedia. This article suggests that it’s working so far (update, link to the article added), The first examples of this program in action are already online. The journal is hosting an open [...]
A recent paper (couple weeks ago) in PLoS Biology from Hingamp et al. had me intrigued. Entitled Metagenome Annotation Using a Distributed Grid of Undergraduate Students, the lecturers put together a system to teach bioinformatics to undergraduates that uses new unannotated sequences from metagenome projects. As stated in the announcement, This method asks students to [...]
Hey, say you’ve got a bacterial genome you just sequenced in your spare time (hey, the way technology is going, it’s not far off) and you need to do a quick and dirty annotation to get you started. Well, there are several tools out there to do that, predict genes, annotate regions, etc. I’d like [...]
Do you have some favorite genes? Well, of course you do–you are probably a researcher who has in the past worked on some specific genes, or you are interested in groups of genes or genomic regions. Or maybe classes of genes. There is a new resource that provides you with a score of how well [...]
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