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SUMMARY:New bioinformatic resources for taxonomic assignment of metagenomi
 c NGS data: BioMaS\, ITSoneDB and SARMA - Santamaria\, M (CNR)
DTSTART:20140327T141500Z
DTEND:20140327T144500Z
UID:TALK51658@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Co-authors: Bruno Fosso (Institute of Biomembranes and Bioener
 getics\, CNR\, via Amendola 165/A\, 70126 Bari\, Italy)\, Mattia DAntonio 
 (CINECA\, Roma)\, Gabriel Valiente (Algorithms\, Bioinformatics\, Complexi
 ty and Formal Methods Research Group\, Technical University of Catalonia\,
  E-08034\, Barcelona\, Spain)\, Giacinto Donvito (Institute national of Nu
 clear Physics\, Via Orabona\, 4\, 70126 Bari\, Italy)\, Alfonso Monaco (In
 stitute national of Nuclear Physics\, Via Orabona\, 4\, 70126 Bari\, Italy
 )\, Pasquale Notarangelo (Institute national of Nuclear Physics\, Via Orab
 ona\, 4\, 70126 Bari\, Italy)\, Giorgio Pietro Maggi (Institute national o
 f Nuclear Physics\, Via Orabona\, 4\, 70126 Bari\, Italy and Politecnico o
 f Bari\, Via Orabona\, 4\, 70126 Bari)\, Graziano Pesole (Institute of Bio
 membranes and Bioenergetics\, CNR\, via Amendola 165/A\, 70126 Bari\, Ital
 y and Department of Biosciences\, Biotechnology and Pharmacological Scienc
 es\, University of Bari\, Bari) \n\nSubstantial advances in molecular micr
 obiology have been carried out in recent years thanks to Metagenomics. Nex
 t Generation Sequencing (NGS) technologies are massively supporting this a
 pproach but imply\, at the same time\, new hard challenges concerning the 
 analysis of the huge amount of data they produce. In this scenario we pres
 ent three new bioinformatic resources aimed at supporting molecular resear
 ches in advanced analyses of NGS metagenomic data. The first one is BioMaS
  (Bioinformatic analysis of Metagenomic ampliconS)\, a comprehensive pipel
 ine for the taxonomic analyses of meta-barcode sequences. BioMaS\, in its 
 current version\, allows the analysis of both bacterial and fungal populat
 ions through the processing of data obtained by Roche 454 or Illumina plat
 forms. BioMaS will be soon implemented as a very friendly publicly availab
 le web-service. The second one is ITSoneDB\, a curated collection of taxon
 omically annotated ITS1 sequences suitable for metagenomic studies of fung
 al communities. ITSoneDB is available at http://itsonedb.ba.itb.cnr.it/. F
 inally\, SARMA (Species Assignment of Reads from Metagenomic Analysis)\, w
 hose construction is still ongoing\, has been designed for the taxonomic c
 haracterization of metagenomic data produced by shotgun NGS\, particularly
  oriented towards the study of human or other host microbiomes. The pipeli
 ne in the first step carries out serial searches against human\, bacteria\
 , fungi\, protozoa and virus reference sequences\, and then reads uniquely
  mapping to the host are removed. In the second step the taxon assignment 
 of all reads uniquely mapping to the above life domains is carried out. A 
 webservice/Galaxy implementation of SARMA is currently in progress\, enabl
 ing the usage of several heterogeneous computing infrastructure thus remar
 kably optimizing the computational load and run time.\n
LOCATION:Seminar Room 1\, Newton Institute
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