ServicesAt the bioinformatics core facility we provide with services within all major areas in bioinformatics analysis. If you are interested in collaborating with us in other areas related to bioinformatics, do not hestitate to contact us.
High-throughput sequencing In the last few years a range of new technologies have made large scale sequencing of genomes both fast and cost-efficient. At the bioinformatics core facility we are following the development of the analytical methods for handing the enormous datasets that result from high-throughput sequencing. We provide with a range of services related to next-generation sequencing. Typical input: A raw datafile recieved from a sequencer. Typically from a 454, Solexa or Solid platform. Types of analysis: - Mapping reads to a reference genome
- Assembling a genome and generating a consensus sequence
- Gene expression analysis from RNA-Seq data
- Finding protein-DNA contact points from ChIP-Seq data
- SNP, Indel, and gene variant-discovery using targeted- or transcriptome sequencing, and providing with a list of interesting gene variants
- Analysis of DNA methylation from bisulfite sequencing
- Detecting and characterizing miRNAs or other short RNAs from next generation sequencing data
- Finding the number of operational taxonomic units (OTUs), creating phylogenetic trees and assigning species, genus or family information from metagenomic studies of short read data.
- General help with software, pipelines and algorithms related to next generation sequencing
Contact: jonaspau@ifi.uio.no
Sequence analysis
Typical input: one or more nucleotide or amino acid sequences or patterns
Types of analyses:
- Identify sequence homologs in organisms of interest
- Create multiple sequence alignment of sequences
- Simple phylogenetic analysis, tree construction
- Functional analysis of protein/DNA sequences
Contact: torognes@ifi.uio.no
Protein structure analysis
The protein structure analysis services are offered in collaboration with the Structural Biology Core Facility.
Typical input: a protein sequence
Types of analyses:
- Analysis of secondary structure
- Identification of probably disordered regions
- Identification of potential model structures by advanced homology searches, threading, or fold recognition
- Build structural model, if possible
- Analysis of conserved regions and potential active residues
- Prediction of mutagenic effects
Contact: torognes@ifi.uio.no
Analysis of DNA variationTypical input: a selected group of genes Types of analyses: - Identification of predicted and confirmed single nucleotide polymorphisms (SNPs) associated with the gene(s) in various regions (coding regions (synonymous and non-synonymous changes), 5' and/or 3' untranslated regions, introns, upstream and/or downstream of gene) based on databases like dbSNP, HapMap etc. Frequency, position etc.
- Identification of known phenotypes of SNPs
- Prediction of effects of nucleotide changes
Contact: jonaspau@ifi.uio.no
Genetic linkage studiesTypical input: a set of individuals, their genetic profile for a set of SNPs, and associated phenotypes. We use a wide range of tools in our linkage analysis pipeline inc. Alohomora, Merlin, Mega2 and Simwalk2. Typical analyses: - Linkage analysis.
- Haplotype estimation.
- Extraction and evaluation of candidate genes.
Contact: halfdan.rydbeck@rr-research.no
MicroarraysTypical input: a set of raw microarray data from supported technological platforms, including in-house and commercial solutions
Typical analyses: - Maintain and develop a microarray database with some analytical capability
- Availability for advice on choices related to analytical questions and tools
- Provide quality control metrics
- Provide a differentially expressed genes list
- Gene ontology and pathway analysis
- Provide annotation conversion
Supported technological platforms: - NMC-printed slides
- Affymetrix (pipleline script available)
- Agilent
Other platforms supported based on interest and availability of analytical tools.
Contact: vegard@mikromatrise.no
General gene association studiesTypical input: A set of gene names
Analyses: - Identify other genes that may be associated with the given genes based on literature co-citation
- Identify other genes that may be associated with the given genes based on genomic context, phylogenetic profiles etc
Contact: halfdan.rydbeck@rr-research.no
Database access- Provide access to local copies of selected databases
- Provide snapshot access to patient data in defined formats
Contact: morten.johansen@medisin.uio.no
Web services
Contact: morten.johansen@medisin.uio.no
|
The facility provides access to locally developed software
tools, databases and web services, ... 
... assists in general sequence analysis of DNA
and protein sequences, ...  ... provide services for analysis of microarray data
on selected techology platforms, ... 
... as well as help its users with modelling protein
structures and predict the phenotypic effects of residue
changes. 
Typical output from a linkage analysis run..... 
..and the corresponding haplotypes in an interesting region. Given millions of short sequences obtained from next-generation sequencing platforms, we can use sophisticated software to map the reads to reference genomes, and detect the interesting parts of the data set. 
|
