Efficient algorithms for the identification of miRNA motifs in DNA sequences
Nuno D. Mendes,
INESC-ID Lisboa and IST –
In the last decade, a novel gene expression regulatory mechanism was discovered. It is mediated by RNA molecules named miRNAs and it acts by silencing target genes. Despite the advancements in this research field, we are still not able to rigourously characterise miRNA genes in order to identify the sequence, structure or contextual requirements that are needed to obtain a functional miRNA.
In this work we present a strategy to sieve through the vast amount of stem-loops that can be found in metazoan genomes, significantly reducing the set of candidates while retaining most known miRNA precursors. The approach relies on a combination of robustness measures, on the analysis of precursor structure, and on the incorporation of information about the transcription potential of each candidate.
The methodology was applied to the genomes of Drosophila melanogaster and Anopheles gambiae, and to homologs of known precursors in the newly sequenced Anopheles darlingi. We obtain, thus, a restricted and ordered set of candidates for these organisms which fulfil the established prerequisites.
Keywords: miRNA, gene finding, single-genome, robustness, stability, secondary structure
Date: 2011-Apr-01 Time: 14:00:00 Room: 020
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INESC Lisboa 2023 Annual Meeting
On November 3rd will take place the first Meeting of INESC Lx, a consortium of the INESC institutions based in Lisbon: INESC-ID, INOV and INESC MN.
The event will take place at Hotel Golf Mar, in Vimeiro, giving all the participants the opportunity to discuss and share the work being developed at INESC Lx. The agenda includes in the Opening Session the President of the Commission for Regional Development and Coordination of Lisbon and Tagus Valley (CCDR LVT), Teresa Almeida and in the Closing Session the Portuguese Minister of Economy, António da Costa Silva.
If you are a member of INESC Lx you can register here by September 29th.
About INESC Lisboa
INESC Lisboa is a unique research consortium in Portugal, representing INESC-ID, INESC MN and INOV, research institutions in the areas of computer science, electronics and computer engineering, and physics engineering in Lisbon. Its mission is to facilitate synergies among the institutes to promote the Research, Development, and Innovation (R&D+i) made in Portugal.
OLISSIPO Workshop: “Metabolism and mathematical models: Two for a tango”
The 3rd Edition of the workshop “Metabolism and mathematical models: Two for a tango” will take place online on November 14-15, 2023.
The topic of the workshop is metabolism in general. As in the previous cases, a special focus will be placed on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects of metabolism, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
More details will soon be provided but initial information may be already found here.
- Barbara Bakker (Faculty of Medical Sciences, University of Groningen, The Netherlands)
- Igor Cestari (Institute of Parasitology, McGill University, Montréal, Canada)
- Vassily Hatzimanikatis (École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland)
- Steffen Klamt (Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany)
- Ina Koch (Goethe Universität, Frankfurt am Main, Germany)
- Laura-Isobel McCall (San Diego State University, US)
Besides the talks given by the above Keynote speakers, there will be two sessions, one per day, of 30 minutes each, dedicated to a discussion of some specific open questions. More details on these will be provided very soon.The workshop will take place in the afternoons, from 2pm to 5:30pm CET time.