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W.M. Keck Facility
Yale University
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Resource Laboratories:
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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:
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Lasergene 7.2
(from DNASTAR), is 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.
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Ingenuity Pathways Analysis 3.1 (from Ingenuity Systems), is used to
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. (note: Usage is
fee-based)
Data
sheet
documentation library
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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. 3 concurrent
user licenses available. (note: Usage is
fee-based)
Data sheet
Software available within the Bioinformatics
Core:
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Genespring GX 7.3 & 9.0
(from Agilent), provides powerful, accessible statistical
tools for fast visualization and analysis of expression data.
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. (note:
Usage is fee-based)
Getting Started Guide (52 pages, 356K) ;
Quick Start Guide ;Tutorial
Manual (970 pages, 10.4M)
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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
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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 microarray 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. (note: Usage is
fee-based)
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Pipeline
Pilot (from Accelrys) is a bioinformatics workflow/pipelining
application. Users can create data processing networks composed of separate
components for data retrieval, filtering, mining. It allows the integration
of software tools from different vendors into a single pipeline for
automated sequential applications, with minimal programming knowledge.
(note: Usage is fee-based)
Product data sheet
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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.
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SYBYL 8.0 (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 (note:
Usage is fee-based)
Overview brochure;
Tripos Bookshelf (lots of documents and tutorials)
Fees
Presentations:
Location:
Sterling Hall of Medicine, Rm. IE53 & IE54
24/7 access controlled by key card
Staff:
| Mark Gerstein, Ph.D. |
Director |
| Hongyu Zhao, Ph.D. |
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
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