Test Case Title

Improved cell factories

Test Case Acronyme: FAIRE-seq


Test Case Class

Microbial and Plants

Contact person

Dr Mikko Arvas, VTT Technical Research Centre of Finland



Test Case Description

We carry out basic and applied research of eukaryotic cell factories in order to understand production of and better produce metabolites and proteins required by bioeconomy. For example we study production of monomers for novel plastics by yeast, production of cellulolytic enzymes for biofuel production by filamentous fungi and production of pharmaceuticals by plants. In order to discover novel enzymes and novel metabolic pathways and to learn to improve the performance of eukaryotic cell factories we study genomes of bacteria, fungi and plants. We use proprietary and public genome sequences, however producing standard basic annotation i.e. genes and protein families etc. for eukaryotic sequences is major impediment for our work. A public resource from which to retrieve and with which to produce such annotation would be gravely needed. Secondly, in order to understand the metabolism of cell factories we need to explore and model it. The standard tool of biological data analysis and modeling, R, however lacks high quality interfaces and programming libraries for this task.

Background knowledge




Initial state of the Test case

Genome sequences produced by various tools, oligonucleotide microarray data

Desired final state of the Test Case

-SBML support in R -interface to STRING, KEGG, Metacyc and SEED in R -easy way (like microbesonline) to get the following info for non-model organisms from databases: chromosome/scaffold sequences, gene sequences and chromosomal coordinates, protein sequences, InterPro functional predictions, protein clustering for getting started in ortholog/paralog searches

Test Case Work Plan




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