From Bioinformatics Core Wiki
Revision as of 18:02, 30 October 2012 by Thermoso (Talk | contribs)

We currently offer different types of services for internal and external users:

Basic services

· Consultation on bioinformatics methods and resources

· Software evaluation, implementation, and training

· Customization of bioinformatics resources

· Training on different bioinformatics topics

Advanced services

Data analysis

  • High-throughput data analysis of genomics, transcriptomics, epigenetics and proteomics datasets
  • Next-Gen data analysis. The unit has invested time and effort in establishing several pipelines dedicated to the analysis of Deep-sequencing data. Currently, the unit has experience analyzing different types of deep-sequencing data:
  1. ChIP-Seq
  • Transcription factor binding site detection / motif discovery
  • Analysis of histone modifications
  • Identification of target genes
  • Data Visualization
  1. High-resolution nucleosome positioning
  2. Detection of Chromosomal Interactions (5C)
  3. RNA-Seq
  • Differential expression at the gene and transcript level
  • Detection of rare, or novel transcripts
  • Identification of alternative splicing and report of isoform abundance
  • microRNA / Small RNA analysis (profiling and discovery)
  • De-novo transcriptome assembly
  • Data visualization
  1. Variation Detection
  • SNP calling
  • Indel calling
  • Variation filtration
  • Functional impact assessment
  • Data visualization
  1. De novo genome assembly
  • Downstream analysis for the interpretation of gene lists, including gene set enrichment, GO and pathway analysis, orthology prediction
  • Identification of functional elements in the genomes:
    • Automatic gene annotation (including non-coding genes)
    • Regulatory sequences: DNA motif analysis (novel and known)
  • Evolution of proteins:
    • Multiple Sequence Alignments
    • Orthology assignments
    • Protein structure comparisons
    • Fold Recognition
    • Phylogenetic analysis

Software Development and Data Management

  • Database design and development
  • Web interface development
  • Development of versatile ticketing and project management systems based on wiki technologies
  • Implementation of integrative bioinformatics web applications
  • Implementation of customized Genome browsers
  • Support for submission of raw data to public repositories (ENA, SRA, GEO..)
Bioinformatics Core Facility @ CRG — 2011-2022