Internet Databases II
Bert Gold, Ph.D., F.A.C.M.G.
The Santa Cruz Website
• The Golden Path
– How Constructed
– Reliance upon the NCBI assembly
– Additional Wash U. data and data from The
SNP Consortium
Santa Cruz Continued
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Add a track, annotation
Utility of the Browser
Demonstrating the use of the Browser
Showing the Repeats, annotation
Looking at Genes, coding regions and
introns
• BLAT
Polymorphism
• STRs
• Segmental Duplications
• Cytogenetics
• Contiguous Gene Syndromes
• Deletion by ‘illegitimate recombination’
(non-homologous recombination)
More Polymorphism
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Mapping
Validating
The Utility of Spidey
Acembly
Automated polymorphism
scoring software
• An excursion away from Internet
• Cluster analysis
– Threshold
– QA/QC
– Binning
– Outliers
• SDS 2.0 and Automated calls
Sequencing for
Polymorphism Detection
• Polyphred
Microsatellite Software
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GeneScan
Genotyper
EXPORT as EXCEL
IMPORT as VNTR
How ‘Phenotype’ is ‘Genotype’ for
Software developers
Genome Assembly Programs
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Phred, Phrap, Consed, Autofinish
Polyphred as a spin-off
Free: The Staden Package
http://www.angis.org.au/Staden/staden_home.html
Free: http://www.generunner.com
Soren Rasmussen’s DNA Tools:
http://www.dnatools.dk
• The Wisconsin Package
• Lasergene
• Sequencher
Database Management Programs
• Cyrillic
http://www.exetersoftware.com/cat/cyrillic.html
• Genomica
• Finch Server
• More Generic
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Microsoft ACCESS
FoxPro
FileMaker
MySQL
• Industrial Strength
– Microsoft SQL
– Oracle
Linkage analysis Generally
• Jurg Ott’s Lab: http://linkage.rockefeller.edu
• Daniel Weeks Lab at Pittsburgh:
http://www.hgen.pitt.edu/
(and then click through on his name)
• Duke University Center for Human Genetics
http://www.chg.duke.edu/software/index.html
More Linkage Analysis Sites
• Genetic Data Analysis Software (Bruce Weir)
http://lewis.eeb.uconn.edu/lewishome/software.html
Comparative Genomics
• HOMOPHILA: HUMAN TO
DROSOPHILA DATABASE
• http://homophila.sdsc.edu/
• JOINT GENOME INSTITUTE (FUGU
HOME)
• http://jgi.doe.gov
• FRUITFLY GENOME PROJECT HOME
• http://www.fruitfly.org
Whole Genome Projects
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Human (www.nhgri.nih.gov)
Drosophila (www.fruitfly.org)
Mouse (www.informatics.jax.org)
Worm (www.wormbase.org)
Yeast (www-genome.stanford.edu)
Rice (www.arabadopsis.org)
Maize (www.agron.missouri.edu)
EBI is responsible for human
gene annotation (officially)
• Ensembl Project
• Hosted at Sanger Center/EBI
The Sanger Center itself is at:
– www.sanger.ac.uk
• Automatic annotation
– www.ensembl.org
How to automate HTML
(HTML Forms)
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Function calls in HTML
PERL
JAVA
C
Applets
Other possibilities (Mathematica)