A recurring theme on the Haskell mailing lists is how to quicly parse a file consisting of integers. Often, this comes up in the contest of benchmarking, but a real example of integer-filled files are the quality data that often accompanies Fasta sequence files. When investigating one of my programs that seemed a bit on [...]
Posted on August 31st, 2009 by ketil
Filed under: Examples, Optimization, Uncategorized | No Comments »
Pyrosequencing is often referred to as next-generation sequencing (although it would be increasingly more accurate to refer to traditional Sanger sequencing as previous-generation sequencing) as it produces large amounts of sequences at lower costs. As the technology is radically different, so are the type of data that results from it, and while it is possible [...]
Posted on July 3rd, 2009 by ketil
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Dephd is a small application for performing various analysis of nucleotide sequences. Originally, it was used for analyzing/converting PHD-file output from the basecaller phred, but it has since grown a bit beyond that. A new update was just pushed onto HackageDB, this is just a quick note describing new features.
Posted on June 16th, 2009 by ketil
Filed under: EST analysis, Uncategorized | No Comments »
Until now (version 0.3.5) of the bioinformatics library, the Sequnce data type has essentially been a wrapper around a couple of strings, with only the most rudimentary and generic structure. This has the advantage that you can easily work with different kinds of sequences without caring about the particulars, but of course, nothing stops you [...]
Posted on May 14th, 2009 by ketil
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In my vacation, I experimented with phantom types for the Sequence data type. Bascially, we want nucleotide and protein sequences to have the same representation, and mostly use the same algorithms, but sometimes we need to distinguish them, so as not to inadvertently treat a protein as a nucleotide sequence. A more detailed writeup is [...]
Posted on March 13th, 2009 by ketil
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Time flees. It’s already been a while since PADL in Savannah, where I had the opportunity to enjoy talks in topics I mostly managed to follow and meet interesting and interested people. Thanks to the organizers and committees making it all possible. I presented a paper on Bloom filters that Bryan O’Sullivan and I wrote, [...]
Posted on February 11th, 2009 by ketil
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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 intermediate product may prove useful [...]
Posted on August 14th, 2008 by ketil
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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 you ask, it was all [...]
Posted on July 31st, 2008 by ketil
Filed under: Uncategorized | 1 Comment »
Posted on April 25th, 2008 by ketil
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