Difference between revisions of "Services"
From Bioinformatics Core Wiki
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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:'' | ||
| − | + | : 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: | * 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:
Contents
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..)
