|
W.M. Keck Facility
Yale University
300 George Street
Addresses
Contact Us
Other
Resource Laboratories:
Yale Cancer Center
Transgenic Mouse
and Gene Targeting Resource
Yale Microarray
Database
Listing of
YSM Core Labs
Department of
Genetics
Department of Molecular Biophysics
& Biochemistry
| |
|
Keck
Home Page > Bioinformatics Resource
Bioinformatics Resource
Current Services:
- Assistance with and support of existing
software provided by the Bioinformatics Core.
- Consultation on DNA/protein sequence,
microarray, protein structure, pathway analysis.
- Collaborative work on bioinformatics
projects.
Current Software:
The use of the software below is free (except
for Lasergene) to the Yale community. Some software is loaded on PCs at the
Bioinformatics Core, others can be used remotely, either through client
programs or with a Web browser.
Network Licensed Sequence Analysis Software:
-
Lasergene 7.2
(from DNASTAR), a comprehensive suite of programs for analysis of
DNA/RNA/protein sequences including sequence editing, sequence assembly,
sequence alignment, primer design, protein structure prediction, and gene
detection and annotation. 15 concurrent user licenses available. (note: Use
of Lasergene licenses is fee-based.)
Instructions, FAQs, tutorials,
case studies, etc.
-
Gene Construction Kit
2.5.13
(from Textco Biosoftware)
, a tool for designing, drawing, and annotating DNA sequences especially
plasmid constructs. 5 concurrent user licenses available.
Tutorials
-
Ingenuity Pathways Analysis 3.1 (from Ingenuity Systems), Analyze
microarray and proteomics data in the context of pathways. This is a
web-hosted application and knowledge base manually curated from the
literature. Users can integrate with other upstream software particularly
statistical/visualization packages, such as Genespring, Partek genomics, SAS-Jump
Genomics, Spotfire. Focused on human, mouse and rat only. 5 concurrent user
licenses available.
Data
sheet
documentation library
-
MetaCore (from Genego),
is an integrated software suite for functional analysis of experimental
data. The scope of data types includes microarray and SAGE gene expression,
SNPs and CGH arrays, proteomics, metabolomics, Y2H and other custom
interactions. It is based on a manually curated database of protein-protein,
protein-DNA and protein-compund interactions, metabolic and signaling
pathways, and effect of bioactive molecules on gene expression.
Data sheet
Software available within the Bioinformatics
Core:
-
Genespring GX 7.3
(from Agilent), helps answer biological questions at the intersection of
genomics, genetics, proteomics, and biomarker screening. It is designed to
integrate data and results from multiple applications, the platform provides
comprehensive statistical analysis, data mining, and visualization tools to
answer a wide range of research questions.
Getting Started Guide (52 pages, 356K)
Quick Start
Guide
Tutorial
Manual (970 pages, 10.4M)
API tutorial (36 pages, 290K)
-
Genespring GT 7.3 (from Agilent), is a desktop analysis workbench
for analyzing high-volume, high-density genotyping data. Designed for the
biologist and the statistician alike, GeneSpring GT is capable of importing,
visualizing, and analyzing hundreds of thousands of variation measurements
simultaneously, for rapid localization of disease or phenotype markers.
Data analysis
flow chart
Features
Quick Start Guide (38 pages, 439K)
User guide (431 pages, 3.2M)
-
HelixTree Genetic Analysis (from Golden Helix), HelixTree
incorporates a host of association tests and methods to uncover significant
associations between genetic variations and disease, drug response or other
clinical outcomes.
Data Sheet
Tutorial
-
GPMAW (from
Lighthouse Data) is used for protein mass analyses including searches of
MS/MS and MALDI data against imported databases or sequences, generation of
theoretical protein digests and the resulting peptide masses, and compiling
amino acid compositions from protein sequences.
Documentation
-
Partek Genomics Suite (from Partek) is a comprehensive suite of
advanced statistics and interactive data visualization specifically designed
to reliably extract biological signals from noisy data. Partek GS's
powerful statistics and interactive data visualization capabilities can be
used to easily analyze and compare a variety of genomic data sets, such as
gene expression data, exon data, copy number data, mapping data, tiling data
and SNP data.
-
VIBE
(from Incogen) is a bioinformatics workflow/pipelining application. Its
bioinformatics toolkit enables the creation of complex data processing
workflows by connecting modules containing various sequence analysis
algorithms. A software development kit enables the creation of new modules
based on data analysis scripts developed in-house.
Product data sheet.
-
Pipeline
Pilot (from Accelrys) is a bioinformatics workflow/pipelining
application. Create data processing networks composed of separate components
for data retrieval, filtering, mining. Integrate software tools from
different vendors into a single pipeline for automated sequential
applications.
Product data sheet
-
SYBYL 7.3 (from Tripos) is a comprehensive tools for molecular
modeling: structure building, optimization, and comparison; visualization of
structures and associated data; annotation, hardcopy and screen capture
capabilities; and a wide range of force fields. It includes SYBYL, to build,
optimize, compare and visualize structures, interface for other modules; and
MOLCAD, to visualize molecular surfaces and molecular properties
Short brochure
Tripos Bookshelf (lots of documents and tutorials)
Presentations:
Location:
Sterling Hall of Medicine, Rm. IE53 & IE54
24/7 access controlled by key card
Staff:
| Mark Gerstein, Ph.D. |
Co-Director |
| Hongyu Zhao, Ph.D. |
Co-Director |
Can Bruce, Ph.D.
Yong Kong, Ph.D. |
Associate Director
Associate Director |
Contact:
Email (preferred contact method):
bioinformatics@yale.edu
Phone: 737-1416 or 737-5011
|
|
