engleski

Genomic data analysis - "What Would Google Do?

Traditionally genome sequencing was an expensive activity. It was carried out by specialised institutes, with the aim of producing a generic genomic annotation, which would then be used as a genetic map for many other research groups interested in the organism. Sequencing institutes maintained a bioinformatics team to carry out the annotation. The dramatic fall in sequencing costs means that genome sequencing is tending to become an experimental technique, which is used as part of the strategy for tackling a research problem, rather than an aim in itself. Thus, the aim of each genome project is different and not satisfied by the provision of a generic annotation. Individual research laboratories or even most biotechnology SMEs do not have the experience and infrastructure in bioinformatics to effectively solve the problems posed by the analysis of genome sequences. Although sequencing service providers can undertake an assembly of the sequence and provide some basic standard annotation, both processes are error-prone and the results need to be critically evaluated. The low cost of genome sequencing is leading to an explosion of sequence information available in the web resulting in problems with search strategies, which may make the recognition of the most relevant information nearly impossible. We see this situation as a market chance for bioinformatics service providers and have started developing a novel expert system for genomic sequence analyses. Our strategy can be described as a bioinformatics "black box design". The user is only interested in whether the system can solve his problems and is not interested in the details of the programs that do the work for him ("black boxes"). Thus, the major emphasis is in designing a human interface that is intuitive and flexible enough for the user to specify the particular problem that he wants to solve. This has obvious analogies to the general searching for information on the internet and we found ourselves repeatedly asking a single question best put by the title of a recent book from Jeff Jarvis: "What Would Google Do?".

Genome sequencing; genomic annotation; sequencing service providers; bioinformatics

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