Student receives fellowship for summer 2016

Alex-NordAlex 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:

RNAcentral now uses nhmmer for searches

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.

A powerful HMMER for data mining

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.”)

Say hello to Dfam1.4

With Dfam, we are striving to build models of repeat families that yield high sensitivity without undue false annotation.  In this release of Dfam, we have improved our model building strategy to reduce the potential for false annotation, especially in the context of overextending alignments around true interspersed repeat instances.

Go to the Xfam blog to read the rest … (Say hello to Dfam1.4.)

Graduate student going to England for Summer Research Position


Outstanding senior and soon-to-be UM Computer Science graduate student Rutger Evans is heading to England. He’ll spend almost three months this summer performing research at the European Bioinformatics Institute (EMBL-EBI), located a few miles down the road from Cambridge, UK.

Rutger will join EMBL-EBI’s Protein Families team, jointly advised by Rob Finn (Protein Families Team Lead) and Alex Mitchell (InterPro Content Coordinator).

Continue reading

Building Momentum in Missoula

It’s been a good first year in the Computer Science Department at the University of Montana, in amazing Missoula. I’ve had the pleasure of teaching great students and been fortunate to build a nice little research group consisting of some really talented people (a PhD student, a couple Masters students, and three Undergrads). We’ve started to make some nice progress on research related to translated search in HMMER, improvements to the application of fast text indexes (esp. the FM index) to remote homology search, and annotation of Transposable Elements. I’ll write more about both the students and their research projects in future posts.

Continue reading