Athurva Gore
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