Athurva Gore: Difference between revisions

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* Received CpG island probe code from Dr. Zhang.
* Received CpG island probe code from Dr. Zhang.
* Need to make modifications discussed in meeting:
* Need to make modifications discussed in meeting:
*Necessary modifications:
* Necessary modifications:
**Remove bisulfite conversion function - DONE
** Remove bisulfite conversion function - DONE
Create dummy function that simply does not do a replacement, but creates fwd and rev strands
[code]Create dummy function that simply does not do a replacement, but creates fwd and rev strands
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.[/code]


**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 Zhang's functions)
** 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
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
Simply modify to adjust so that A has high Tm, B has low Tm
Simply modify to adjust so that A has high Tm, B has low Tm
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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 17:06, 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

[code]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.[/code]

    • 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