Research Seminar Dr. Rob Finn (UK)
Dentmed Research Seminar Series
Dr Rob Finn, Protein Families Team Leader, European Bioinformatics Institute (EMBL-EBI), United Kingdom
Title: Shedding light on billions of metagenomics sequences: challenges, pitfalls and discovery
Host: Margaret Sällberg Chen
The EBI metagenomics portal contains over 60,000 consistently analyses datasets, encompassing both a wide range of biomes and experimental approaches. The free-to-use service, allows the archiving and analysis of metagenomics, metatranscriptomics, assemblies and amplicon data. Approximately three-quarters of the datasets housed in EBI metagenomics represent amplicon experiments, the remaining quarter are large scale shotgun metagenomics datasets. These datasets can run in to 10s TBs of raw sequence and represent technical challenges in scalability of analysis. As sequence families have generally scaled linearly over time, coupled with algorithmic and technical developments, they represent one of the most efficient ways to reveal the functional potential of a microbial community. The use of the InterPro and Rfam databases to consistently annotate datasets, and how we use the results to allow the mining and discovery of metagenomics data will be presented. Such work demonstrates that there is much still to be understood and modelled by protein families. Nevertheless, investigating the unannotated metagenomics sequences, termed the ‘Dark Matter’, reveals much of the ‘Dark Matter’ may not all be novel sequences. Some of the preliminary results of a new comparison tool will also be presented.
The seminar is in English.
Please register by Monday November 14 if you want a salad. NB. No drinks will be served!Contact person: Heli Vänskä