Molecular Pathology Division Related Links

Sequence Analysis

  • dCAPS Finder
    (Mismatch PCR Primer Design Tool) A program from Washington University to design mismatch PCR primers for the detection of SNP's by simple restriction enzyme digestion and electrophoresis. The web-based program is described by Neff, Turk , & Kalishman TIGS 18:613-15, 2002.
  • SSCP Analysis
    Access to new software, QUISCA, for the analysis of capillary array SSCP data (free for academic users!) from Professor Hayashi's laboratory. QUISCA is Quantitative Interpretation of SSCP in Capillary Array and is described in BioTechniques 33:1342-8, 2002.
  • Searching GenBank
    Search GenBank, dbEST (expressed sequence tag database) dbSTS (sequence tagged site database), or dbGSS (genome survey sequences database).
  • BioToolkit
    Jump station to Internet servers- 3 categories, Nucleic Acid Analysis, Genome Resourses, and Protein Structural Imaging and Analysis.
  • BLAST
    Search the public databases for homology to any sequence using BLAST.
  • ExPASY
    ExPASy (Expert Protein Analysis System) is the proteomics server of the Swiss Institute of Bioinformatics (SIB) dedicated to the analysis of protein sequences and structures as well as 2-D PAGE

Genomics

  • UniGene
    UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
  • Genome Gateway
    A comprehensive web resource devoted to genomics maintained by the Nature publishing Group.
  • Genomics Glossaries
    A very nice set of glossaries for Genomics, Pharmacogenomics, Proteomics, and Structural Biology. At the Cambridge Healthtech Institute (CHI) site. Use the buttons on the right of the frame to go to the Genomic Glossaries. 

 Genetics

  • The Lieden Muscular Dystrophy page
    This site contains a lot of useful information on the genes and proteins involved in hereditary muscular dystrophy. Includes mutation/polymorphism databases and detailed protocols for molecular analyses.
  • GeneTests
    Listing of clinical laboratories offering genetic testing.
  • Cystic Fibrosis Mutation Database
    Compilation of mutations in the CFTR gene maintained by Dr. Lap-Chee Tsui.
  • DNA Learning Center
    Introduction to DNA and genetics at Cold Spring Harbor Laboratory.
  • Breast Cancer Information Core
    Compilation of mutations (and methods) associated with inherited forms of breast cancer.
  • The National Tay-Sachs & Allied Diseases Association
    (NTSAD ) is dedicated to the treatment and prevention of Tay-Sachs and related diseases, and to provide information and support services to individuals and families affected by these diseases, as well as the public at large.
  • CAP Sample Exchange Registry
    The CAP Sample Exchange Registry for Alternative Assessment is an Internet-based service designed to connect laboratories performing esoteric genetic testing where no formal proficiency testing is available.  When at least three laboratories are identified as testing for the same genetic disorder, the CAP will facilitate the sample exchange.

Pharmocogenetics and Pharmocogenomics

Metabolic Pathways

Cancer

  • OncoLink
    Founded in 1994 by Penn cancer specialists with a mission to help cancer patients, families, health care professionals and the general public get accurate cancer-related information at no charge.
  • The Cancer Genome Anatomy Project
    (CGAP) is an interdisciplinary program established and administered by the National Cancer Institute to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.

HIV

  • AIDS Knowledge Base
    An on-line textbook on HIV disease from the University of California, San Francisco and San Francisco General Hospital
  • HIV Sequence Database
    A database maintained at Los Alamos National Laboratories of HIV genome sequences, including an on-line tool for the identification of drug resistance mutations in user submitted sequence.
  • Stanford HIV RT and Protease Sequence Database
    An on-line tool for the identification of drug resistance mutations in user submitted sequence.

HCV

  • CDC
    Hepatitis homepage . Educational site on hepatitis at the CDC

Microarray Technology

  • DRAGON
    Online software for the annotation and analysis of microarray data from the Professor Prevsner's lab at the Kennedy-Kreiger Isntitute. DRAGON is Database Referencing of Array Genes Online.
  • Brown Lab Homepage
    Homepage for one of the guru's of the field- includes instructions for building your own arrayer!

Organizations

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