Harvard:Biophysics 101/2007/04/19

—smd 23:39, 18 April 2007 (EDT)
 * Same drill as last week. Post what you plan to do on your personal page, and link to it below with 1-line summary.
 * Remember to organize your links so we can easily review your progress in class.

Plans
 * Chris Write SNP sequence parser and integrate QC code. Propose ideas for OMIM non-hits.
 * Zach Finish CDC prevalence 4-24 completion / consolidate CDS mutation code from earlier (delayed) / determine CDS from a gene input or blast search  4-26 almost complete
 * Tiff Learn how to & parse HTML and XML to extract info from MedStory searches
 * Cynthia Think about how to deal with non OMIM hits, as in the context of what was discussed in class on Thursday
 * Resmi Finish code to parse out keywords from Pubmed and think about how we can process non-OMIM hits.  4-24 Progress; 4-26 Progress
 * Xiaodi Genbank file parsing to work around issues with OMIM; will hopefully fetch genes of note and characterize SNPs
 * Deniz Bringing in the news, trials, news and such and keep working on the ranking.
 * Michael Still examining the possibility of estimating allele frequency and maybe penetrance based on Hapmap data combined with epi studies of particular SNPs present within a given allele for a sequence. Also starting to code up something that will make a polyphen query to handle sequences not in OMIM but found in BLAST and get back some idea of whether or not the mutation may be deleterious.