Internet Databases I Bert Gold, Ph.D., F.A.C.M.G..

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Presentation transcript:

Internet Databases I Bert Gold, Ph.D., F.A.C.M.G.

Browsers Browsers must be Java Enabled and able to accept cookies Netscape –Do not use NETSCAPE 6.0 or above! Microsoft Internet Explorer Operasoftware

Search Engines Northernlight has indexed the largest number of sites on the web. Google search has recently taken over the Deja news archive, which includes bionet.* An NNTP server is valuable for serious developers.

NCBI NCBI at the National Library of Medicine at NIH The Online Mendelian Inheritance of Man (OMIM) –Contains descriptions and up-to-date references concerning specific diseases, traits and genetic mechanisms.

FTP File Transfer Protocol is indispensable for genetic research Several forms of Windows interface are available at MACs have their own FTP interfaces and all MS-OS comes with ftp.exe

OMIM Entry Description Each OMIM entry has a unique six-digit identifier –The first digit indicates the mode of inheritance 1= autosomal dominant 2= autosomal recessive 3= X-linked 4= Y-linked 5= Mitochondrial 6= Refers to autosomal loci or phenotypes created after May 1994

OMIM Statistics

OMIM Allied Resources Cross References –Coriell Human Genome Nomenclature Home Page Davis Human/Mouse Homology Map Online Mendelian Inheritance in Animals (OMIA) Alliance of Genetic Support Groups Human Gene Mutation Database (HGMD) Jackson Lab FlyBase

More OMIM Linked Databases RetNet: Genes causing retinal diseases MitoMap at Emory HUM-MOLGEN listserv Locus Specific Databases Eg- Patched Cystic Fibrosis GeneClinics (

LOCUS LINK Links to: OMIM dbSNP Genbank Taxonomy RefSeq GeneCards

NBLAST nr htgs

The many faces of BLAST Psi-BLAST TBLASTN Hashing generally

The Merck Manual

PCR Primer Design MIT’s Primer Programs Considerations MeltCalc

How to GRAB an IMAGE On Microsoft Operating Systems –Hit Print Screen Key –Open Powerpoint –Paste On Macintosh Systems –Apple+Shift+3 means capture entire screen to file –Apple+Shift+4 means capture a single window to a file –This results in a PIC file, which can be pasted into applications.

Vector Drawing pDRAW32 Plasmid Premier Visual Cloning Clone Map for PC Bioedit Gene Construction Kit

Sequence Tagged Sites and Polymorphisms GDB Genethon ftp://ftp.genethon.fr/pub/Gmap/Nature-1995ftp://ftp.genethon.fr/pub/Gmap/Nature-1995 MIT NCBI Research Genetics ATCC Location Data Base Marshfield Map-o-mat (automates CRI-MAP via a web interface)