Resources Quick Links
Cores
- Advanced Microscopy Facility
- Bioinformatics Core
- Biomolecular Research Facility
- BioNMR Spectroscopy Core Facility
- Biorepository and Tissue Research Facility (BTRF)
- Biostatistics Core
- DNA Sciences Core
- Flow Cytometry (FACS) Core
- Gene Targeting and Transgenic Facility
- Lymphocyte Culture Facility
- Mass Spectrometry Core
- Molecular Assessment and Preclinical Studies (MAPS) Core
- Molecular Imaging Core
- Protein Sciences Core
- Research Histology Core
- Tissue Culture Facility
- W.M. Keck Biomedical Mass Spectrometry Core
Centers, Institutes, and Other Research Facilities
- Asthma & Allergic Diseases Center
- Cancer Center
- Carter Immunology Center
- Center for Alcohol & Substance Education
- Center for Biomathematical Technology
- Center for Biomedical Ethics and Humanities
- Center for Cell Signaling
- Center for Global Health
- Center on Health Disparities
- Center for Immunity, Inflammation and Regenerative Medicine
- Center for Molecular Design
- Center for Public Health Genomics
- Center for Research in Reproduction
- Center for the Study of Neurodegenerative Disease
- Diabetes Center
- Diabetes and Hormone Center of Excellence
- Digestive Health Research Center
- Division of Perceptual Studies
- General Clinical Research Center
- Human Immune Therapy Center
- Institute of Law, Psychiatry & Public Policy
- International Health Care Worker Safety Center
- Keck Center for Cellular Imaging
- Myles H. Thaler Center for AIDS & Human Retrovirus Research
- Nephrology Clinical Research Center
- Paul Mellon Prostate Cancer Research Institute
- Robert M. Berne Cardiovascular Research Center
Other Support Facilities
- Bioinformatics Core
- Center for Comparative Medicine
- Clinical Trials Office
- Health Sciences Library
- Research Computing Lab
Policies
- Environmental Health and Safety
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- UVA Office of Sponsored Programs
Resources
3. Analyzing Your Data
Biomolecular Data
Sequence Homology Searching Online
BLAST
searches
NCBI is the primary Web site for BLAST
FASTA
searches
The European Bioinformatics Institute (EBI) hosts the primary web site
for FASTA searches
Contact: Michael Black, PhD, mblack@virginia.edu
WU-BLAST2
server
Also hosted by EBI
Contact: Michael Black, PhD, mblack@virginia.edu
Finding specific sequences on the web
DNA sequences
Note that GenBank, EMBL, and the DDJB are all synchronized daily
GenBank
(NCBI)
GenBank® is the NIH genetic sequence database, an annotated
collection of all publicly available DNA sequences
Search GenBank using NCBI's integrated search engine ENTREZ
Contact: Michael Black, PhD, mblack@virginia.edu
European
Molecular Biology Laboratory's EMBL database
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank)
constitutes Europe's primary nucleotide sequence resource. Main sources
for DNA and RNA sequences are direct submissions from individual
researchers, genome sequencing projects and patent
applications.
Contact: Michael Black, PhD, mblack@virginia.edu
DNA Databank
of Japan (DDBJ)
DDBJ is one of three summit databanks that construct the
DDBJ/EMBL/GenBank International Nucleotide Sequence Database.
Contact: Michael Black, PhD, mblack@virginia.edu
Protein sequences
Protein sequence data are primarily available via UniProt,
the Unified Protein Knowledgebase
ExPaSy
The ExPASy (Expert Protein Analysis System) proteomics server of the
Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of
protein sequences and structures as well as 2-D PAGE
Contact: Michael Black, PhD, mblack@virginia.edu
Protein
Information Resource Center (PIR), Georgetown
University Medical Center
An integrated public bioinformatics resource to support genomic and
proteomic research, and scientific studies
Contact: Michael Black, PhD, mblack@virginia.edu
NCBI's
ENTREZ integrated search system
ENTREZ can be used to find predicted structures. Also has a free viewer
(Cn3D) for download
Contact: Michael Black, PhD, mblack@virginia.edu
Sequence Analysis
Tools available at the UVA Bioinformatics Core
Access to GCG suite of tools
Command line, UNIX X graphical interface, or Web based via Seqlab
Contact: Michael Black, PhD, mblack@virginia.edu
EMBOSS
collection of applications
Open source collection comparable to GCG. On UNIX and Apple OS X
machines, EMBOSS can be run in a Java graphical environment using the
JemBoss package. Command line EMBOSS also available on the Bioinformatics Core's server
watson.achs.virginia.edu
Contact: Michael Black, PhD, mblack@virginia.edu
Online Resources
Other freely available resources:
San Diego
Supercomputer Center
Online sequence analysis workbench server
Contact: Michael Black, PhD, mblack@virginia.edu
European
Bioinformatics Institute
Numerous analysis tools
Contact: Michael Black, PhD, mblack@virginia.edu
Institut
Pasteur
Numerous analysis tools
Contact: Michael Black, PhD, mblack@virginia.edu
Genomic Analysis
Other freely available resources:
NCBI's
genomic resources
Tools and databases for working with genomic data
Contact: Michael Black, PhD, mblack@virginia.edu
Sanger
Institute and EBI's Ensemble Genome Suite
Genome suites
Contact: Michael Black, PhD, mblack@virginia.edu
UCSC
Genome Browser tools
Genome browser tools
Contact: Michael Black, PhD, mblack@virginia.edu
Sequence Alignment
ClustalW
Widely used multiple sequence alignment programs available at
command
line on watson.achs.virginia.edu. Can be freely downloaded from
ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Contact: Michael Black, PhD, mblack@virginia.edu
Structure Prediction
PDB
Known protein structures can be viewed and downloaded
Contact: Michael Black, PhD, mblack@virginia.edu
ExPASy
Tools for predicting protein structure and viewing simulated structures
(Swiss-PdbViewer, aka DeepView)
Contact: Michael Black, PhD, mblack@virginia.edu
NCBI's
ENTREZ integrated search system
ENTREZ can be used to find predicted structures. Also have free viewer
(Cn3D) for download
Contact: Michael Black, PhD, mblack@virginia.edu
Function Prediction
NCBI's
RefSeq database
See "Sequence Homology Searching online" above
Contact: Michael Black, PhD, mblack@virginia.edu
The Pfam data-
base (Protein Family)
The Pfam data-base (Protein Family)
Contact: Michael Black, PhD, mblack@virginia.edu
Transcription factors
TRANSFAC
database
TRANSFAC® 7.0 Public 2005 contains data on transcription
factors, their experimentelly-proven binding sites, and regulated
genes. Its broad compilation of binding sites allows the derivation of
positional weight matrices.
Contact: Michael Black, PhD, mblack@virginia.edu
TESS
search tools
TESS is a web tool for predicting transcription factor binding sites in
DNA sequences. It can identify binding sites using site or consensus
strings and positional weight matrices from the TRANSFAC, JASPAR, IMD,
and our CBIL-GibbsMat database. You can use TESS to search a few of
your own sequences or for user-defined CRMs genome-wide near genes
throughout genomes of interest.
Contact: Michael Black, PhD, mblack@virginia.edu
McPromoter
gene
promotor searching tool
McPromoter is a program aiming at the exact localization of eukaryotic
RNA polymerase II transcription start sites.
Contact: Michael Black, PhD, mblack@virginia.edu
Gene Expression Profiling/Microarray
Data generated by the Biomolecular Research Facility (BRF) are
sent directly to the Bioinformatics Core.
Investigators access their data via the Affy LIMS systme (an account will be created by BRF staff when you first place an order)
Contact: Michael Black, PhD, mblack@virginia.edu
GEOSS home page
Contact: Michael Black, PhD, mblack@virginia.edu
Non-commercial gene expression analysis software
GenePattern
(BROAD Institute at MIT)
Comprehensive, modular package for gene expression analysis
Contact: Michael Black, PhD, mblack@virginia.edu
Expression
Profiler at the EBI
An online set of R-based tools for microarray analysis
Contact: Michael Black, PhD, mblack@virginia.edu
dChip
One of the oldest and established open-source packages (requires
Windows OS) developed by Drs. Li and Wong
Contact: Michael Black, PhD, mblack@virginia.edu
TM4 suite
Open source set of programs (Java based) developed originally by
scientists at TIGR (now the J. Craig Venter Institute) and the
Dana-Farber Cancer Institute and Harvard School of Public Health
TM4 is targeted to researchers with 2-color array data (especially the
Data Manager tool, MADAM), it can also be used to analyze Affymetrix
data
Contact: Michael Black, PhD, mblack@virginia.edu
R and
Bioconductor
R is an open source software environment for statistical computing and
graphics, and Bioconductor is a suite of open source R tools
specifically for genomic data analysis, including gnee expression data.
This approach to expression data analysis is arguably the least user
friendly, but allows the use of a large selection of analysis tools.
Contact: Michael Black, PhD, mblack@virginia.edu
Pathway analysis
GenMapp
Free computer application from the Gladstone Institutes to visualize gene expression
data on maps of biological pathways
Contact: Michael Black, PhD, mblack@virginia.edu
Gene expression databases
NCBI's
Gene Expression Omnibus (GEO)
Other gene expression databases
There are also numerous organism specific and pathological-based gene
expression databases that can be found by simple key word Web searches
Contact: Michael Black, PhD, mblack@virginia.edu
Example:
Mouse embryo gene expression map
Contact: Michael Black, PhD, mblack@virginia.edu
Example:
mouse brain database
Contact: Michael Black, PhD, mblack@virginia.edu
Example: E.
coli gene expression database at the University of Oklahoma
Contact: Michael Black, PhD, mblack@virginia.edu
A
searchable registry of genome projects
Contact: Michael Black, PhD, mblack@virginia.edu
Genome/Model Organisms
Genome/model
organisms
Check for information about a specific genome project at the Genome Online Database (GOLD).
Genome Browsers
UCSC's
genome browser
Provides entries to specific organism's genome resources
Model organisms have many additional resources, such as
Yeast (Saccharomyces cerevisiae) database
Mouse resources at the Jackson Laboratory
Sanger Instite model organizm genome sites
Microbes
Bacterial genomes at the Sanger Institute
Comprehensive Microbial Resource at the J. Craig Venter Institute (formally TIGR)
Plants
The cowpea (Vigna unguiculata) genome
The rice (Oryza sativa) genome project
The corn (Zea mays) genome project
Phylogenetics
PHYLIP
Command line suite of tools for analyzing all types of phylogenetic
data. The Bioinformatics Core maintains the complete PHYLIP package on our primary
molecular biology server watson.achs.virginia.edu
Contact: Michael Black, PhD, mblack@virginia.edu
Institut
Pasteur
Online tools for phylogenetic analysis
Contact: Michael Black, PhD, mblack@virginia.edu
Tree of Life
Project
Phylogenetic/taxonomic information on organisms
Contact: Michael Black, PhD, mblack@virginia.edu
Clinical Data
UVa
Center for Survey Research
CSR is a full-service survey research facility, offering: customized
project design, from sampling to instrument development, Professional
interviewing and data collection using the latest survey technologies,
and data analysis and report preparation.
Contact: surveys@virginia.edu
Health Services Data
Spatial
and Statistical Data and Services (Scholars' Lab, UVA Library)
Specialized software for GIS and statistical analysis
Contact: Kelly Johnston, MS GIS, kgj3t@virginia.edu
Research
Computing Lab (UVA Library)
Software and Consultation services in a wide variety of technologies
and methodologies for high performance and research computing.
Contact: Andrew Sallans, MLIS, als9q@virginia.edu
Tissue
Tissue
Microarrays (Biorepository and Tissue Research Facility)
Tissue microarray technology places up to a thousand discs of tissue on
a single glass slide, which can then be assayed by histologic staining,
immunohistochemistry and/or in situ hybridization.
Contact: Craig Rumpel, MS, Biorepository Manager, crumpel@virginia.edu