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

• 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

• 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

• GeneScan

• Genotyper

• EXPORT as EXCEL

• IMPORT as VNTR

• How ‘Phenotype’ is ‘Genotype’ for Software developers

Genome Assembly Programs • 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

– 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

• 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)

• Function calls in HTML

• PERL

• JAVA

• C

• Applets

• Other possibilities (Mathematica)