Services

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

2) High-resolution nucleosome positioning

3) Detection of Chromosomal Interactions (5C)

4) 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

5) Variation Detection

· SNP calling

· Indel calling

· Variation filtration

· Functional impact assessment

· Data visualization

6) 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)
  • Functional annotation of protein 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..)