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Keck Home PageBioinformatics 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

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Last modified: 20-Dec-2006 (GB)