Novel bioinformatics resources for microbial genomics for synthetic biology

It might be assumed that the genomics and bioinformatics tools and resources needed to underpin synthetic biology design are robust and well established. This is not the case. Genome sequence information is of widely varying quality. Sequenced strains are not always readily available, or are associated with restrictive material transfer and licensing agreements. Annotations are inconsistent with regard to gene naming conventions, gene positioning, and various other differences that make them difficult to use. And, bioinformatics tools have frequently been developed for what might be called ‘descriptive genomics’, which is often not fit for purpose when it comes to dissecting systems in the detail necessary to provide a basis for knowledge- based design. For this reason, we place a heavy emphasis on the underpinning genomics and bioinformatics for our synthetic biology strategies.

Areas of work have included:

• Sequence assembly optimization
• New sequence annotation strategies for the strain collections and underpinning the comparative behavioural genomics strategy
• New analytical approaches to assessing evolving populations under selection
• New approaches to bacterial typing and population genetics
• New ways to address the ‘true core’ genome to support metabolic modelling for design
• New data summary / compression techniques to support comparative behavioural genomics
• New methods to address time-series transcription studies