Harvard:Biophysics 101/2007/Project

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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.

Outline

Path 1: Using OMIM

Sequence -> RS Number (dbSNP)

RS Number -> Mesh Terms(OMIM)

Mesh Terms -> Disease Name (in-house code, search engines)

Disease Name -> Useful Patient Info (in-house code, medical search engines)

Path 2: Using GenBank and PolyPhen

Sequence -> Genomic Position (BLAST)

Genomic Position -> Gene(s) of Interest(GenBank)

Gene -> Mutations (in-house code)

Mutations -> Disease Name (PolyPhen and/or OMIM)

Project-in-Progress

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

Project Ideas

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