castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



Quarterly Activity Report -- Hinxton Sequence Forum Wellcome Trust Genome Campus

A quarterly activity report for the different activities that take place under what can be considered "sequence" at the WTGC in Hinxton, Cambridge, UK:

  • HGNC has made great progress in solving nomenclatures for 130 cases where the community has a diversity of opinions and it's difficult to agree on something. Very good point in saying that in the Internet era it's better to give a gene a name that is distinctive to common words that would clobber your Google search results. There is now a forum set up for different communities to use in discussions for gene family names.
  • Havana now has started using RNAseq data to confirm new genes found in human and zebrafish that didn't have evidence before. One new feature is a "confirmed intron" for when paired Solexa reads bridge two exons, with an associated score for read depth. Confident this type of data will bring out many interesting new annotations that couldn't be found before, e.g. genes expressed in a given tissue during a lapse of a few hours in the development. There are already a few examples in zebrafish.
  • Wormbase has been working hard on compiling more data from the modENCODE. Small but cool infrastructure achievement in having VMware images running for old releases that investigators can just pull and bring up on demand.
  • Ensembl Genomes has been successfully testing the beta sites for Bacteria, Protists and the first Metazoa build. Another Metazoa build is in progress, with all the phylogenetics goodness of the 12 Drosophila genomes plus the vectors plus C.elegans and a few other outgroups. The modENCODE project is about to complete the re-annotation of gene models using CAGE data that will bring more precise gene starts for melano and elegans. Ensembl Genomes is still working together with Manchester and now the US to put together an Aspergillus resource that provides the best value for money to researchers. PombBase is also being pursued, lots of labs interested in having it Ensemblified and ready to use.
* This is a personal blog. Things said here are not to be taken as official reports.

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