Northern Germany these days experiences many hundreds of infections with severest clinical symptoms by a new strain of E. coli bacteria EHEC subtype. The genome has recently been sequenced only to find out that it is something novel, featuring the EHEC surface markers with something from African strains. No, antibiotics don't work, yes, the number of cases are still increasing, no, the source has not been found.
What would be great to have readily available for everyone are now tools to present some comparative genomics of that strain against the other strains of E. coli sequenced so far. I was very happy to read here http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/ about collaboratively analysing the raw sequencing data. The next step would then be to look at strain differences and interpret them - on the molecular level and in the clinical context. So, whatever tools we could help promoting to the more clinical researchers, they might be used for a while.
I am not completely sure about what Debian Med could help best with. So, much in line of some earlier blog entry on "doing things with Debian Med" I ask just anyone in contact with researchers working with E. coli (or other pathogenic bacteria) to report on what tools they would like to have available through us or what tools they are already using that Debian Med does not yet provide (so other can have it more easily).
Update [10th of June]: Through the Bioinformatics Computation group at LinkedIn I was pointed to http://enews.patricbrc.org/1172/e-coli-outbreak-new-comprehensive-comparisons/. It looks very nice though I have not any idea yet about how to work with it. And I learned about yet another tool, RAST, standing for 'Rapid Annotation using Subsystem Technology'. More comments, please.
Update [14th of June]: A group in Saarbuecken focuses on regulatory transcriptional motifs of EColi.
Prof. Kurtz kindly pointed me to the MOSAIC database (http://genome.jouy.inra.fr/mosaic/) to which one of his tools had contributed that is now substituted by CoCoNUT (http://toolcoconut.org/, http://www.biomedcentral.com/1471-2105/9/476). MOSAIC is just sadly last curated in 2010, otherwise the community effort could possibly end just there. So we'd need to perform those runs ourselves, just CoCoNUT we cannot redistribute with its current license and it will take too long to be clarified.
ReplyDeleteTo the creation of MOSAIC contributed a second tool MAUVE (http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html). This looks also real nice. I will be investigating to prepare it as a package over the next couple of days.
More ideas? Just drop them here, please.