Seminar: Searching for distant homologs of small, non-coding RNAs
2012-03-14: by Robert Giegerich, Center of Biotechnology and Faculty of Technology, Bielefeld University. At 14:00. in auditorium A2-84.-11, building 2-84, Thorvaldsensvej 40, University of Copenhagen, LIFE, Frederiksberg.
Registration is not necessary. Refreshment will be served.
Our appreciation of the functional repertoire of noncoding RNA has increased enormously in recent years. Present RNA-sequencing projects yield a large number of bonafide small RNA transcripts, calling for bioinformatics approaches to lter out promising candidates for experimental study. Potential interaction partners and phylogenetic conservation can provide additional evidence. However at present, there is no fully automated solution either problem. In the SNAP project (Small Non-coding RNA in Alphaproteo-Bacteria), we identified about 1000 small ncRNA transcripts in S. meliloti . Aside from confirmation of small ncRNAs known with S. meliloti at that date, search of the Rfam data base with covariance models brought little extra information. 52 trans-encoded RNA transcripts were chosen, for which 39 new family models were build with a mixture of automated and hand-crafting methods. The talk gives an overview of our ndings and then concentrates on two candidate ncRNAs that are widely distributed in the Rhizobiales, but cannot be detected with standard methods. Given that we have Internet connection, the talk will end with the audience creating their own search program for finding distant ncRNA homologs.
The SNAP project is joint work with Jan Reinkensmeier, Anke Becker, and Jan-Philip Schlüter