Tag Archives: Software

Poster on Exomate at GfH 2014 in Essen

exomate-posterExomate: an easy to use exome sequencing analysis pipeline

Christopher Schröder, Johannes Köster, Christoph Stahl, Sebastian Venier, Sven Rahmann, Marcel Martin

Exomate is an exome-sequencing pipeline with a web frontend. It automates most steps needed to go from FASTQ files to variant calls, puts the calls and metadata about patients, samples, etc. into a database and then allows interactive analysis via a web frontend. It is primarily designed for easy use and has already been used in various studies [1,2,3].

[1] Martin, M. et al., 2013. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat. Genet. 45, 933–936.

[2] Czeschik, J.C. et al., 2013. Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome. Hum. Genet. 132, 885–898.

[3] Voigt, C., et al., 2013. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies – expanding the phenotypes associated with EFTUD2 hfg mutations.
Orphanet J Rare Dis 8, 110.

 

Christopher Schröder presents a poster at Science Day 2013, University Hospital Essen

Target identification for metabolic engineering,

Christopher Schröder, Sven Rahmanntarget-poster

In metabolic engineering by gene knockouts, one searches for genes controlling metabolic reactions that should be removed from a metabolic network in order to optimize the yield of a desired metabolite.

In a conservative way, this is done by undirected mutagenesis selection of the population with best efficiency.

Unrean et al. developed a simple algorithm to directly predict reaction targets, to save the high costs of this uncontrolled expensive process. It is based on elementary modes, undecomposable sequences of metabolite transformation flows in the network.

We substantially improved the algorithm and applied it to a network of Escherichia coli to show the improved results.