Archive for February, 2013

Non-redundant prokaryotic genomes

We just had an Applications Note accepted in Bioinformatics. The little note presents a tool we develped to choose sets of non-redundant prokaryotic genomes (see Research-Genome Clusters too).

The tool derives from previous work where we selected sets of non-redundant prokaryotic genomes filtered at different levels of similarity for such tasks as displaying results on operon predictions, to finding the level of filtering out redundancy to maximize the number of high-quality predicted associations by phylogenetic profiles. Other groups have been using our non-redundant sets. Thus, we thought it was better to share to the wider community and we developed this tool. If you have suggestions for improvements, please let us know. We cannot promise to implement all suggestions, but we will try to make the tool very useful. Also note that the R-scripts used to produce these datasets are provided (as is). These might help you develop your own datasets if so you require.


Paraphernalia available

I changed the “palette” page into a “paraphernalia” page (see menu). A page where I will be putting any little file that might be useful to other research groups and such. Example, a PERL module with variables holding color-blind friendly color palettes, or LaTeX templates, et cetera. All offered “as is.” Very little in there now, but might grow.

That’s it.


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