Transcript 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.
• 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
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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
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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
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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
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GDB http://www.gdb.org
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Genethon ftp://ftp.genethon.fr/pub/Gmap/Nature-1995
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MIT http://www-genome.wi.mit.edu/
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NCBI
Research Genetics
ATCC
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Location Data Base
http://cedar.genetics.soton.ac.uk/public_html/ldb.html
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Marshfield
http://research.marshfieldclinic.org/genetics
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Map-o-mat (automates CRI-MAP via a web interface)
http://compgen.rutgers.edu/mapomat/