http://blog.malde.org bioinformatics and haskell Thu, 20 Nov 2008 11:01:36 +0000 http://backend.userland.com/rss092 en Roche's 454 sequencing technology can produce biological sequence data on a scale that exceeds traditional Sanger sequencing by orders of magnitude.   Due to the fundamentally different method used to generate the sequences, we would like to investigate the raw data and see if we can quantify -- and maybe also ... http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/ I've been spending the last couple of weeks working on an indexing scheme for sequences, using Bryan O'Sullivan's Bloom filters.  Now, it turned out that when Bryan tested out the code, he found a curious problem:  Apparently, the indexing stage scaled quadratically with sequence length.  This wouldn't have been so ... http://blog.malde.org/index.php/2008/10/24/optimization-again-befuddled-by-bytestrings/ It was just brought to my attention that people have started to use a new file format for sequences.  This format, called 'FastQ' combines both the sequence data itself and the quality data in one file.  That's a nice idea, and I implemented support for it, tests, docs and all, ... http://blog.malde.org/index.php/2008/09/09/the-fastq-file-format-for-sequences/ In my copious spare time, I've started putting together a tutorial for using the biohaskell library.  It'll probably take some time -- anything from a while to an eternity -- until it's complete, but I thought I'd follow the adage of "release early, release often" in the hope that the ... http://blog.malde.org/index.php/2008/08/14/the-wee-beginnings-of-a-biohaskell-tutorial-and-some-thoughts-on-programming-productivity/ Bloom filters is apparently a relatively old technology, dating from the 1970s or so, but it has somehow escaped my radar until Bryan O'Sullivan posted a message to the haskell mailing list announcing a high-performance implementation in Haskell, perhaps to support a chapter in the upcoming book.  You can read ... http://blog.malde.org/index.php/2008/07/31/a-plan-for-bloom-filters/ Just some quick notes: Hackage submissions updated There seems to have been problems with some of the bioinformatics applications on Hackage, thanks to Don S. for pointing it out. That should be fixed now by new uploads, but I'm still waiting for the automatic builds to register results. An, since ... http://blog.malde.org/index.php/2008/07/31/updates-and-other-trivialities/ My current development project is an EST pipeline.  For various reasons, it is implemented in shell --- bash, to be exact.  In other words, the pipeline is a script, or rather a set of scripts, that will tie together the various stages: masking, clustering, assembly, and annotation. As in any program, ... http://blog.malde.org/index.php/2008/07/11/functional-bash-bracketing/ As a consequence of IWC policies, the Institute of Marine Research is required to store genetic identification of each minke whale that is hunted. This of course means that people will come to me for help in bridging the gap between test tubes and the databases by providing some ... http://blog.malde.org/index.php/2008/05/27/giving-users-what-they-want-haskell-scripts-on-the-web-with-cgi/ It seems to be optimization week on the haskell café mailing list. Inspired by a combination of Don Stewart's blog post about how to optimize for speed and the sorry performance of my xml2x program, I thought this would be good time to see if things could be ... http://blog.malde.org/index.php/2008/05/18/optimization-week-making-haskell-go-faster/ ...to write a simple, but useful and efficient bioinformatics program? Here's how to build a simple tool to extract a clustering from an ACE file, using functionality in the bioinformatics library. It is about three lines of actual code, it is fast, and it is efficient. http://blog.malde.org/index.php/2008/05/09/can-you-spare-five-minutes/