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Internet Databases II

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

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Internet Databases II

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

  2. The Santa Cruz Website • The Golden Path • How Constructed • Reliance upon the NCBI assembly • Additional Wash U. data and data from The SNP Consortium

  3. 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

  4. Polymorphism • STRs • Segmental Duplications • Cytogenetics • Contiguous Gene Syndromes • Deletion by ‘illegitimate recombination’ (non-homologous recombination)

  5. More Polymorphism • Mapping • Validating • The Utility of Spidey • Acembly

  6. Automated polymorphism scoring software • An excursion away from Internet • Cluster analysis • Threshold • QA/QC • Binning • Outliers • SDS 2.0 and Automated calls

  7. Sequencing for Polymorphism Detection • Polyphred

  8. Microsatellite Software • GeneScan • Genotyper • EXPORT as EXCEL • IMPORT as VNTR • How ‘Phenotype’ is ‘Genotype’ for Software developers

  9. 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

  10. 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

  11. 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

  12. More Linkage Analysis Sites • Genetic Data Analysis Software (Bruce Weir) http://lewis.eeb.uconn.edu/lewishome/software.html

  13. 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

  14. 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)

  15. 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

  16. How to automate HTML (HTML Forms) • Function calls in HTML • PERL • JAVA • C • Applets • Other possibilities (Mathematica)

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