22–26 Sept 2008
Harbiye Askeri Museum
Europe/Zurich timezone

Experiences on metagenomic analysis using the EGEE grid

23 Sept 2008, 14:45
15m
Kocatepe Hall (Harbiye Askeri Museum)

Kocatepe Hall

Harbiye Askeri Museum

Istanbul

Speaker

Dr Ignacio Blanquer (UPV)

Description

The execution of BLAST runs of metagenomes with respect to annotation databases, such as the Non Redundant (nr) from the NCBI provides many interesting results, such as the incoherencies in the annotation of entries in the reference databases [1] or the definition of more precise phylogenetic trees. In the frame of EGEE, the UPV has developed in collaboration with the Institute Cavanilles for Biodiversity, a framework for splitting, data distributing, execution and monitoring of BLAST runs on metagenomes. The framework enables replicating reference databases, compiling BLAST executable on the fly and automatic resubmission. The large size of data blocks to be retrieved and analyzed (on the order of 2Gb for the reference databases) and the need for downloading, compiling and locally installing software is a difficult test for many resources, which could fail on executing parts of the experiment. Since all need to be finished, the resubmission engine has been intensively tested. Currently, the system has executed experiments consuming more than 5 CPU years with metagenomes of gut, virus, soil and oceanic samples. [1] Miguel Pignatelli, Gabriel Aparicio, Ignacio Blanquer, Vicente Hernández, Andrés Moya and Javier Tamames, "Metagenomics Reveals our Incomplete Knowledge of Global Diversity", Bioinformatics, ISSN 1367-4803, Oxford University Press 2008.

Authors

Dr Ignacio Blanquer (UPV) J. Tamames (Instituto Cavanilles de la Biodiversidad - Universidad de Valencia) M. Pignatelli (Instituto Cavanilles de la Biodiversidad - Universidad de Valencia) Vicente Hernandez-Garcia (Polytechnical University of Valencia)

Presentation materials