links - CBRG, Oxford University

Computational Biology Research Group

University of Oxford

Links

CBRG Home

CBRG Accounts (molbiol)

Analysis tools

Training courses

Collaborative data

Oxford-only section

FAQ: CBRG + UNIX

FAQ: Bioinformatics

External Links and Resources

Bioinformatics | Biology links pages | Genomes | Journals | Microarrays
Nucleotide databases | Oxford | Phylogenetic trees | Protein databases SAGE | Sequence analysis | Sequence similarity searches | Transcription

Bioinformatics

Bioinformatics databases - databases featured in Nucleic Acids Research
Bioinformatics.Org - open organisation to host collaborations in bioinformatics
BioPlanet - Bioinformatics - forum, news, companies, jobs, courses
EMBOSS - Open Source software for sequence analysis
European Multimedia Bioinformatics Educational Resource (EMBER)
- EMBER bioinformatics tutorial (requires login)
GCG manual - version 10.3
IUPAC single-letter, nucleotide codes
Staden - Sequencing Project Management package
Public CVS repository - from Sanger
Perl modules documentation for bioperl-1.4
- bioperl tutorials - including, SearchIO, SeqIO and graphics
Perl modules documentation for Ensembl
- Ensembl perl API tutorial

Biology links pages

123genomics - genomics, proteomics and bioinformatics links
functional genomics - collection of links for functional genomics, bioinformatics, microarrays, proteomics etc
Cambridge bioinformatics - bioinformatics-related courses at Cambridge

Genomes

BioMart - genome data mining at Ensembl
GOBASE - organelle genome database
GOLD - Genomes Online Database
MBGD - database for comparative analysis of completely sequenced microbial genomes
The Genome Sequencing Center - Washington University Medical School
TIGR - The Institute for Genomic Research

Browsers:
- Ensembl - genome browser at EBI / Sanger
- mapview - genome browser at NCBI
- UCSC - genome browser at UC Santa Cruz

Mouse:
- MGI - Mouse Genome Informatics - The Jackson Laboratory, USA
- NIH - Trans-NIH Mouse Genomics and Genetics Resources
- NCBI
  - NCBI - Mouse Genome Resources
  - NCBI - Human/Mouse Homology Relationships

Journals

Microarrays

ArrayExpress - public repository for microarray data at the EBI
BASE - (BioArray Software Environment), a web-based database for data generated by microarray analysis (free)
- BASE Analysis Tutorial at Harvard University
- BASE Plug-in descriptions - at Massachussetts General Hospital
Bibliography - microarray data analysis papers
Data mining DNA microarrays - links page on www.gene-chips.com
GEO - (Gene Expression Omnibus) online gene expression data browsing at the NCBI
GNF SymAtlas - Genomics Institute of the Novartis Research Foundation
MIAME - Minimum Information About a Microarray Experiment (Nature Genetics)
MGED - Microarray Gene Expression Data Society
SMD - Stanford Microarray Database

Nucleotide databases

DDBJ - DNA Data Bank of Japan
EBI - European Bioinformatics Institute (EMBL)
NCBI - National Center for Biotechnology Information (GenBank, Pubmed, OMIM etc.)
dbSNP

Oxford

Dunn School - Sir William Dunn School of Pathology
Oxford Immunology Group
Oxford International Child Health Group
OCMS - Oxford Centre for Molecular Sciences
- Oxford events - of interest to OCMS scientists
OUCS - Oxford University Computing Services
Therapeutic Immunology Group - (TIG) Immune tolerance research
- Therapeutic Antibody Centre - (TAC) CAMPATH-1 antibody studies
WIMM - Weatherall Institute of Molecular Medicine
Wellcome Trust Centre for Human Genetics

Bioinformatics at Oxford:
- Bioinformatics and Statistical Genetics - Wellcome Trust Centre for Human Genetics
- Bioinformatics MSc - part-time degree at Oxford University CPD
- Man-Suen Chan - Human Anatomy and Genetics
- David Gavaghan - Oxford University Computing Laboratory (OUCL)
- Jotun Hein - Genome Analysis & Bioinformatics Group, Department of Statistics
- Peter Jeavons - Oxford University Computing Laboratory (OUCL)
- Richard Mott - Wellcome Trust Centre for Human Genetics
- Chris Ponting - MRC Functional Genetics Unit
- Ioannis Ragoussis - Core Genomics Group, Wellcome Trust Centre for Human Genetics
- Stephen Roberts - Department of Engineering Science
- Mark Sansom - Laboratory of Molecular Biophysics
- David Shotton - Bioimage Database, Department of Zoology

Phylogenetic trees

Introduction to Phylogenetic Analysis - Society of Australian Systematic Biologists
Tutorial - how to make a phlyogenetic tree
Introduction to Trees and Multiple alignments
Trees and ClustalW

Protein databases

CATH - hierarchical classification of protein domain structures
DALI -3D protein structure comparisons
ExPASy - protein sequence analysis tools and databases

SWISS-PROT - curated protein sequence database (also, TrEMBL & UniProt)
PROSITE - database of protein families and domains
ENZYME - enzyme nomenclature database
Proteomics tools

InterPro - database of protein families, domains and functional sites
PDB - 3-D structure data of proteins and nucleic acids
PFAM - manually curated collection of protein families
UniProt - (Universal Protein Resource). Swiss-Prot, TrEMBL, and PIR databases combined

Serial Analyis of Gene Expression - SAGE

Human Transcriptome Map - visualization of gene expression levels on a chromosome
SAGE Genie - at NIH
SAGEmap - resource of SAGE data from any organism at NCBI
SAGEnet

Sequence analysis

STARS - Sequence Typing Analysis and Retrieval System
MLST - Multi Locus Sequence Typing

Sequence similarity searches

BLAST at NCBI

Transcription

Promoters:
- PROSCAN - Predicts promoters using homologies with putative eukaryotic Pol II promoters
- NNPP - (Neural Network Promoter Prediction)
- Promoter 2.0 Prediction Server
- Eponine Transcription Start Site finder
- RSA Tools - (Regulatory Sequence Analysis) detect regulatory signals in non-coding sequences

Transcription factor binding sites:
- JASPAR - Database of transcription factor binding site profiles
- ConSite - Explore transcription factor binding sites shared by two genomic sequences
- TESS - Predicts transcription factor binding sites in DNA sequences using the TRANSFAC, JASPAR, IMD, and CBIL-GibbsMat database
- Weeder - Excellent general purpose motif finder that scans several sequences for common motifs.
- RVista - Looks for regulatory regions based on conserved elements
- Toucan 2 - Based on Ensembl ids or uploaded sequences looks for regulatory regions in selected sequence or orthologs. Requires Java to be installed.
See also:
- Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques (2006) Genome Res. 16:1455-1464