Difference between revisions of "Services"

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(Created page with "''We currently offer different types of services for internal and external users:'' == Basic services == · Consultation on bioinformatics methods and resources · ...")
 
(Data analysis)
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* High-throughput data analysis of genomics, transcriptomics, epigenetics and proteomics datasets
 
* 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
+
* 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
 
* 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
2)  High-resolution nucleosome positioning
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# High-resolution nucleosome positioning
3)  Detection of Chromosomal Interactions (5C)
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# Detection of Chromosomal Interactions (5C)
4)  RNA-Seq
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# 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
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* De-novo transcriptome assembly
 
* De-novo transcriptome assembly
 
* Data visualization
 
* Data visualization
5) Variation Detection
+
# Variation Detection
 
* SNP calling
 
* SNP calling
 
* Indel calling
 
* Indel calling
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* Functional impact assessment
 
* Functional impact assessment
 
* Data visualization
 
* Data visualization
6) De novo genome assembly
+
#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:
 
** Automatic gene annotation (including non-coding genes)
 
** Automatic gene annotation (including non-coding genes)
 
** Regulatory sequences: DNA motif analysis (novel and known)
 
** Regulatory sequences: DNA motif analysis (novel and known)
** Evolution of proteins:
+
 
* Multiple Sequence Alignments
+
* Evolution of proteins:
* Orthology assignments
+
** Multiple Sequence Alignments
* Protein structure comparisons
+
** Orthology assignments
* Fold Recognition
+
** Protein structure comparisons
* Phylogenetic analysis
+
** Fold Recognition
 +
** Phylogenetic analysis
  
 
=== Software Development and Data Management ===
 
=== Software Development and Data Management ===

Revision as of 18:02, 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
  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..)
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