Monday, November 17, 2008

Biological Informatics Subject-Tracer Blog

Marcus P. Zillman's Biological Informatics Subject-Tracer Blog contains a long list of web resources. Some of the links are stale, but there's still a lot of good stuff there.

Friday, November 14, 2008

Amino acid "seqlets"

IBM publishes bio-dictionaries of 'seqlets' for a number of organisms. What's that? you ask. According to IBM: "In a number of publications, we have presented and discussed the idea of the Bio-Dictionary: the latter is a collection of recurrent amino acid combinations (='seqlets') which completely cover the sequence space defined by the biggest possible collection of amino acid sequences. Normally, we recompute the contents of the Bio-Dictionary on a regular basis, typically once a year."

Bio-dictionaries for a handful of Archaeal genomes and a dozen or so bacterial genomes are available for download here. Note that the files are in .Z (Unix compression format) form. Don't expect to view them in your browser.

Wednesday, November 12, 2008

IBM open-source bioinformatics tools

IBM Watson Research Center's Bioinformatics & Pattern Discovery Group has a number of interesting online tools (around a dozen in all) for which source code is available. Go to the Brief Tutorials page to get a quick idea of what the tools are all about. Some of them are rather esoteric, but by the same token that also means they're not the run-of-the-mill sequence analysis tools. These are IBM's own special contributions.

Worth checking out.

Tuesday, November 11, 2008

Journal of Proteomics & Bioinformatics

The Journal of Proteomics & Bioinformatics is an Open Access journal. All papers are available for free download in PDF format.