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Internet Databases I

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.

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Internet Databases I

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

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

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. OMIM Statistics

  8. 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

  9. 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)

  10. LOCUS LINK • Links to: • OMIM • dbSNP • Genbank • Taxonomy • RefSeq • GeneCards

  11. NBLAST • nr • htgs

  12. The many faces of BLAST • Psi-BLAST • TBLASTN • Hashing generally

  13. The Merck Manual • The Merck Manual • http://www.merck.com

  14. PCR Primer Design • MIT’s Primer Programs • Considerations • MeltCalc

  15. 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.

  16. Vector Drawing • pDRAW32 http://www.crosswinds.net/~acaclone/index.htm • Plasmid Premier http://www.premierbiosoft.com/plasmidmap/plasmidmap.html • Visual Cloning 2000 http://www.redasoft.com • Clone Map for PC http://www.cgcsci.com • Bioedit http://www.mbio.ncsu.edu/BioEdit/bioedit.html • Gene Construction Kit http://www.textco.com

  17. Sequence Tagged Sitesand 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/

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