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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 • http://www.ncbi.nlm.nih.gov/ • The Online Mendelian Inheritance of Man (OMIM) • http://www.ncbi.nlm.nih.gov/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 www.download.com • 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 (http://www.geneclinics.org) 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 • The Merck Manual • http://www.merck.com 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 http://www.crosswinds.net/~acaclone/index.htm • Plasmid Premier http://www.premierbiosoft.com/plasmidmap/plasmidmap.html • Visual Cloning 2000 • Clone Map for PC • Bioedit http://www.redasoft.com http://www.cgcsci.com http://www.mbio.ncsu.edu/BioEdit/bioedit.html • Gene Construction Kit http://www.textco.com Sequence Tagged Sites and Polymorphisms • GDB http://www.gdb.org • Genethon ftp://ftp.genethon.fr/pub/Gmap/Nature-1995 • MIT http://www-genome.wi.mit.edu/ • • • NCBI Research Genetics ATCC • Location Data Base http://cedar.genetics.soton.ac.uk/public_html/ldb.html • Marshfield http://research.marshfieldclinic.org/genetics • Map-o-mat (automates CRI-MAP via a web interface) http://compgen.rutgers.edu/mapomat/