Athurva Gore

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Revision as of 17:05, 11 August 2008 by >Ajgore
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Lab Rotation

  • Will add daily entries once schedule settles down a bit.

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 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