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We would like to develop software and documentation that will help people get from sequence to diagnosis.  At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise.  We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon.  Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.
We would like to develop software and documentation that will help people get from sequence to diagnosis.  At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise.  We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon.  Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.


=Outline=
 


=Path 1: Using OMIM=
=Path 1: Using OMIM=

Revision as of 17:47, 30 April 2007

Biophysics 101: Genomics, Computing, and Economics

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Overview

  • Project Goal: To develop tools to aid in analysis of personal DNA sequences.

We would like to develop software and documentation that will help people get from sequence to diagnosis. At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise. We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon. Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.


Path 1: Using OMIM

Sequence -> RS Number (BLAST SNP)

  • Xiaodi

RS Number -> Mesh Terms (PubMed)

  • Cynthia

RS Number -> Disease Name (OMIM)

RS Number -> Disease Name (PubMed)

  • Resmi

Mesh Terms -> Disease Name (in-house code, prevalence algorithm)

  • Deniz
Disease Name -> Useful Patient Info (Medical search engines)
  • Deniz and Tiff


Path 2: Using GenBank and PolyPhen

Sequence -> Gene Name (BLAST)

  • Zach

Gene Name -> Mutations (GenBank)

  • Xiaodi

Gene Name -> ??? (PolyPhen)

  • Mike

Mutations -> Disease Name (OMIM)

  • Xiaodi

Disease Name -> Useful Patient Info (Medical search engines)

  • Deniz and Tiff


Diagram

Project Diagram

Project-in-Progress

Project-in-Progress notes have been moved to their own page.

Project Ideas

Project ideas have been moved to their own page.

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