The Wheeler lab has been awarded competitive pilot project funding through the University of Montana Center for Biomolecular Structure and Dynamics (CBSD). The grant will support early development of methods for reducing false sequence annotation of large genomic DNA datasets due to repetitive sequence and alignment overextension, and will fund two students in our group for the next year. CBSD is supported by a National Institutes of General Medical Science (NIH NIGMS) IdeA program Center of Biomolecular Research Excellence (CoBRE) Phase II grant.
Congratulations to lab member Gilia Patterson, who today was recognized as the University of Montana Outstanding Senior in Genetics and Evolution. Gilia has done great work with me on understanding sources of transposable element mis-classification (manuscript coming soon to a theatre near you), and we’re happy as can be for her!
Dfam is growing up. This is the first major expansion of the database since it’s inception. We’ve added repeat families from four new organisms: mouse, zebrafish, fruit fly, and nematode. In total, this release includes 2,844 new familes ( 4,150 total ).
I’m wrapping up a lengthy trip to England and Ireland, in which I had the chance to catch up with a member of the lab, Rutger Evans, who has been working on a summer project at the EBI, under the guidance of one of my favorite collaborators, Rob Finn.
Alex Nord has just been awarded a Center for Biomolecular Structure and Dynamics Graduate Student Fellowship for the summer of 2016. The fellowship will support Alex while he continues research on using spaced seeds to boost both speed and sensitivity in the context of database search with profile hidden Markov models (in HMMER, of course).
Read more at: http://news.umt.edu/2015/06/060915cbsd.php
RNAcentral is an open resource that provides a unified platform for accessing non-coding RNA sequences from a broad range of ncRNA databases. Anton Petrov has just announced a 3rd release. Along with a slew of new features, RNAcentral is now powered by our nhmmer which they’ve found to be more sensitive than Exonerate. They’re using the recently-released HMMER3.1b2, a stable beta release that implements our new accelerated DNA search based on seed finding with the FM index data structure (I’ll describe that here once we get the paper submitted … soon). Exciting days.
New paper describing recent advances in the HMMER web server (primarily driven by the endlessly talented Rob Finn and Jody Clements):
Finn RD, Clements J, Arndt W, et al. (2015) HMMER web server: 2015 update. Nucleic Acids Res. DOI: 10.1093/nar/gkv397
Also, a little love from the EMBL-EBI press machine: A powerful HMMER for data mining. (The last line reads like a call to arms: “The next step for the collaborators is to extend the software to accommodate DNA searches, which involves far larger datasets.”)