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Project #15721
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#15721 : Yersinomics SynTView instance deployment for 85 genomes and development of a SynTView javascript local view
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Name of Applicant : Javier PIZARRO-CERDA
Date of application : 11-09-2020
Unit : Yersinia
Location : Duclaux, RdC Haut, 01A
Phone : 0145688326
@ Mail : pizarroj@pasteur.fr

Project context and summary :

Yersinia pestis, Y. pseudotuberculosis and Y. enterocolitica are major human pathogens. Bacnet is a Java based platform to develop websites for multi-omics analysis. Yersinomics allows comparative genomics and transcriptomics between pathogenic Yersinia species. In the tool a SynTView module is dedicated to study synteny profiles between several strains. We use complete genomic data from Yersinia bacterial strains obtained in the refseq ftp site to compute the orthologs between three pathogenic Yersinia species (Y. pestis, Y. pseudotuberculsis and Y. enterocolitica) with bi directional best hits strategy and use SyntView to do visual genomic comparison. Due to the discontinuation of the use of flash technology on some web-browser, SynTView must be rewrite in another language. Part of the application (snps visualization) is already developed in javascript and will serve as a starting point for the rewrite of SynTView local view.


Related team publications :
Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization. Savin C, Criscuolo A, Guglielmini J, Le Guern AS, Carniel E, Pizarro-Cerdá J, Brisse S. Microb Genom. 2019 Oct;5(10):e000301. doi: 10.1099/mgen.0.000301.
Service Delivery
Project Manager : pierre.lechat@pasteur.fr
Project Type : Medium
Status : Pending


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