Athurva Gore: Difference between revisions
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*** Commented code to find/replace | *** Commented code to find/replace | ||
*** Question: parts we are looking at; do they have N's in them? Probably shouldn't. | *** Question: parts we are looking at; do they have N's in them? Probably shouldn't. | ||
** '''Remove CG score penalty - DONE''' | ** '''Remove CG score penalty - DONE''' | ||
*** in function getProbeList | *** in function getProbeList | ||
*** remove section starting with "my $CG_penalty" | *** remove section starting with "my $CG_penalty" | ||
*** set CG_penalty as always zero for quick fix, remove CG finding code later | *** 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)''' | ** '''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 | *** Looks like function oligoFreq does this; currently just uses log of each side | ||
*** Modify probe score calculation to favor segment B being more unique | *** Modify probe score calculation to favor segment B being more unique | ||
*** See function getProbeList | *** See function getProbeList | ||
** '''Modify score calculation so that Tm of segment A should be high and Tm of segment B should be low''' | ** '''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 | *** At the moment, Tm score is used in p_score calculation | ||
Line 26: | Line 23: | ||
*** See function getProbeList | *** See function getProbeList | ||
*** Specific thresholds? | *** Specific thresholds? | ||
** '''Exon database''' | ** '''Exon database''' | ||
*** Ask about our current UCSC data; it comes in format on PGP server, or is this modified? | *** Ask about our current UCSC data; it comes in format on PGP server, or is this modified? | ||
*** Found Exon-Intron Database; uses GenBank | *** Found Exon-Intron Database; uses GenBank | ||
*** Show Dr. Zhang the readme | *** Show Dr. Zhang the readme |
Revision as of 17:08, 11 August 2008
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 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
- Remove bisulfite conversion function - DONE