At last, a new release. HMMER 3.4 is now available at hmmer.org. The most important thing about 3.4 is that we now support ARM processors, including Apple OS/X ARM M1 and M2 machines, thanks to an ARM port contributed by Martin Larralde at EMBL Heidelberg.
The …
Michael Farrar's striped SIMD Smith/Waterman source code [swsse2; Bioinformatics, 2007], is now available under an open source license for the first time. You can download it [here].
In 2007, Michael Farrar introduced a beautiful method for speeding up sequence alignment algorithms. Farrar's "striped" algorithm rearranges dynamic programming matrix indices …
Congratulations to Jin Kyu Park, who was named last week as the first DACA immigrant to become a Rhodes Scholar. The Rhodes Trust changed its rules because of him. Previously, only US citizens were allowed to apply for the Rhodes. In the spirit of DACA, it seemed like Dreamers should …
No one really knows how the game is played
The art of the trade
How the sausage gets made
We just assume that it happens
A while back Elena Rivas and I posted a response to a bioRxiv preprint (Tavares et al, 2018) that challenged some of the conclusions in …
Harvard's Quantitative Biology Initiative is searching for a new tenure-track assistant professor. This is a broad search -- we don't have any particular focus areas in mind. We are interested in people studying fundamental biological questions using quantitative, computational, theoretical, or experimental methods. The Initiative emphasizes cross-departmental interaction among our life …
A new bioRxiv preprintfrom Rafael Tavares, Anna Marie Pyle, and Srinivas Somarowthu challenges conclusions of our 2017 Nature Methods paper where we describe R-scape, a method for detecting support for conserved RNA secondary structure in sequence alignments by statistical analysis of base pair covariations. In our paper, among other …
HMMER 3.2.1 is now available, fixing some small issues, mostly portability issues having to do with compilation on PowerPC machines and ancient x86 machines.
Thanks to the GCC Compile Farm folks for access to ppc64be and i686 machines that I'm using for testing now!
The glorious master plan was to finish HMMER4 while hoping that HMMER3 stayed stable. Alas, HMMER4 development has been even slower than expected, and bugs and bitrot have accumulated on HMMER3. Here's a new HMMER 3.2 release to tide us all over. I'm managing HMMER releases again, with Travis …
Astronomy began when the Babylonians mapped the heavens. Our descendants will certainly not say that biology began with today's genome projects, but they may well recognize that a great acceleration in the accumulation of biological knowledge began in our era.
Graeme Mitchison wrote those opening lines of our book Biological …
I'm looking for four teaching fellows (TFs) for my course MCB112 Biological Data Analysis in the fall 2018 semester. TFs are typically Harvard G2 or G3 students (second- or third-year PhD students, in Harvard-speak), but can be more senior students or even postdocs. I teach the course in Python and …