Difference between revisions of "Services"

From Bioinformatics Core Wiki
(Data analysis)
(Data analysis)
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* 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:''
 
* 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:''
#ChIP-Seq
+
: 1) ChIP-Seq
* Transcription factor binding site detection / motif discovery
+
:: · Transcription factor binding site detection / motif discovery
* Analysis of histone modifications
+
:: · Analysis of histone modifications
* Identification of target genes
+
:: · Identification of target genes
* Data Visualization
+
:: · Data Visualization
# High-resolution nucleosome positioning
+
: 2) High-resolution nucleosome positioning
# Detection of Chromosomal Interactions (5C)
+
: 3) Detection of Chromosomal Interactions (5C)
# RNA-Seq
+
: 4) RNA-Seq
* Differential expression at the gene and transcript level
+
:: · Differential expression at the gene and transcript level
* Detection of rare, or novel transcripts
+
:: · Detection of rare, or novel transcripts
* Identification of alternative splicing and report of isoform abundance
+
:: · Identification of alternative splicing and report of isoform abundance
* microRNA / Small RNA analysis (profiling and discovery)
+
:: · microRNA / Small RNA analysis (profiling and discovery)
* De-novo transcriptome assembly
+
:: · De-novo transcriptome assembly
* Data visualization
+
:: · Data visualization
# Variation Detection
+
: 5) Variation Detection
* SNP calling
+
:: · SNP calling
* Indel calling
+
:: · Indel calling
* Variation filtration
+
:: · Variation filtration
* Functional impact assessment
+
:: · Functional impact assessment
* Data visualization
+
:: · Data visualization
#De novo genome assembly
+
: 6) De novo genome assembly
* Downstream analysis for the interpretation of gene lists, including gene set enrichment, GO and pathway analysis, orthology prediction
+
:: · 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:
 
* Identification of functional elements in the genomes:

Revision as of 18:04, 30 October 2012

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)
    • 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..)
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