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==August 4th - August 10th== * Received CpG island probe code from Dr. Zhang. * Need to make modifications discussed in meeting: * Necessary modifications: ** '''Remove bisulfite conversion function - DONE''' *** Create dummy function that simply does not do a replacement, but creates fwd and rev strands *** Commented code to find/replace *** Question: parts we are looking at; do they have N's in them? Probably shouldn't. ** '''Remove CG score penalty - DONE''' *** in function getProbeList *** remove section starting with "my $CG_penalty" *** set CG_penalty as always zero for quick fix, remove CG finding code later ** '''Add function to check sequence uniqueness in human genome (build hash table ahead of time, check Dr. Zhang's functions)''' *** Looks like function oligoFreq does this; currently just uses log of each side *** Modify probe score calculation to favor segment B being more unique *** See function getProbeList ** '''Modify score calculation so that Tm of segment A should be high and Tm of segment B should be low''' *** At the moment, Tm score is used in p_score calculation *** Simply modify to adjust so that A has high Tm, B has low Tm *** See function getProbeList *** Specific thresholds? ** '''Exon database''' *** Ask about our current UCSC data; it comes in format on PGP server, or is this modified? *** Found Exon-Intron Database; uses GenBank *** Show Dr. Zhang the readme
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