Genomic Research Laboratory
Division of Infectious Diseases
University of Geneva Hospitals
Rue Gabrielle-Perret-Gentil, 4
CH-1211 Geneva 14 - Switzerland

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Software

   
           
       
   

The purpose of our bioinformatics staff is mainly to solve problems such as microarray design and data analysis by developing an automated approach. Several tools were made for rapid chip design and analysis, in parallel specific algorithms were developed to enhance probes discrimination.

In addition, web interfaces were developed to ease data access and sharing among users:

  1. a local BLAST database which allows us to customize our database with specific clinical sequences (archiving) and also shorten the searching time.
  2. a mini LIMS for archiving and managing microarray experiments.


by D. Hernandez

Edena is an overlaps-graph based de novo assembler dedicated to process the Illumina GA paired-end (short inserts) and mate-pairs (long inserts) dataset.
Last version: EdenaV3.131028 (October 28, 2013)
 
 

by Y.Charbonnier and B.Gettler

Click for details OliCheck is a program designed to test the validity of potential microarray probes by considering the possibility of cross-hybridization with non-target coding sequences. This analysis can be performed within a single genome or between several different strains/organisms.

Software available - with demo input files - for Windows platforms.
 
 
A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.
Charbonnier Y, Gettler B, Francois P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J.
BMC Genomics. 2005 Jun 17;6(1):95. [Abstract] - [PubMed]



by A.Huyghe and Y.Charbonnier

Click for details [Click for Gallery] This software is dedicated to our high-throughput MLVA method (Multi-Locus VNTR Analysis, see Reference below) which was developed for the rapid and affordable genotyping of MSSA and MRSA. This method determines the number of dinucleotide repeats in several genes (currently 10 different targets within a single tube), and separates them using rapid capillary electrophoresis. This approach is coupled to this dedicated interface used for peak detection and data analysis (clustering) providing very high strain discrimination, applicable for outbreak analysis (Harbarth et al., Emerg Infect Dis. 2005 Jun;11(6):962-5.) or prolonged follow-up.
 
 
Use of an Automated Multiple-Locus, Variable-Number Tandem Repeat-Based Method for Rapid and High-Throughput Genotyping of Staphylococcus aureus Isolates.
Francois P, Huyghe A, Charbonnier Y, Bento M, Herzig S, Topolski I, Fleury B, Lew D, Vaudaux P, Harbarth S, van Leeuwen W, van Belkum A, Blanc DS, Pittet D, Schrenzel J.
J Clin Microbiol. 2005 Jul;43(7):3346-55. [Abstract] - [PubMed]


   
     
           
   
           
       
   
Related links
 
Software
  Array Designer
  BLAST
  GeneSpring
  Feature Extraction
 
External Links
  ISREC - Bioinformatics
   
     
           

Revised Nov 20, 2014 - © 2003-2017 Genomic Research Laboratory, Geneva