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Research & Services | The Bioinformatics Unit

Smith Yoav, HUJI, School of Medicine - IMRIC

Categories

Bioinformatics, sequence analysis, genomic data analysis, structural biology bioinformatics

Objective/function

  • The Bioinformatics Unit provides consultation, education and computational services to the Hebrew University biological and medical research community

Research provided

Advantages

  • The Bioinformatics Unit has a highly knowledgeable, skilled staff utilizing state-of-the-art equipment and technologies

Client record

  • Hadassah Medical Center
  • HUJI researchers

Available equipment

Infrastructure

  • New bioinformatics servers: COMBI and OMICS, SGI origin 300, with Irix operating system, connected to a 2 TB storage device 

Software

  • SRS 8.1, with EMBOSS functions embedded, as well as standalone EMBOSS. In addition to the command line SRS and EMBOSS, SRS may be used with a web interface
  • Perl, as well as some modules of BioPerl.
  • Other programs/packages: BLAST, ClustalW, Vienna Package, meme, mast

Databases

  • Nucleotide: EMBL, REFSEQ nucleotides
  • Protein: Niprot: Swissprot and TREMBL; PDB
  • Domain: Prosite, PFAM and Prints
  • Mutations: OMIM

Genomic Analysis

  • Matlab and Perl-based dedicated custom-built server 
  • Special filters and other built image processing packages
  • Statistical analysis, data normalization and clustering are carried out with several software packages: Spotfire, Acuity, Jsota, Genepix, ScanAyze, SAM
  • Custom-packages built using Matlab and Perl
  • Access to free packages such as Bioconductor or Afymetrix and other gene annotation tools

Structural Analysis

  • DS Modeling 1.1 (Accelrys, Inc) molecular modeling programs with modules for
  • Structural visualization and manipulation of biological molecules
  • Model building using homology modeling (Modeler)
  • Molecular dynamics and energy minimization calculations (CHARMm)
  • Electrostatic calculations (GRASP)

Staff

  • Tamar Kahan, PhD
  • Yoav Smith, PhD

Contact

Contact for more information:

Itzik Goldwaser
VP, Head of Research Collaborations
+972-2-6586685
Contact ME:
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