10:30a – 8:15p, 12:00p- 1:00a
Meeting with XZ
- prepping slides (see notes)
Test probes synthesis
- analyze tomorrow
Coding matlab-storm
- Work with Jeff to restructure startup / installation
- need to update readme
- need to update all global variables to new conventions
Probe Design
Issues with Oligo Array
Typical previous run:
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 954 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding CTTCCCATTTGTAGGAATGGAAATAATAACAGTACATATTAT… DONE
Testing specificity… DONE
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 953 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding GCTTCCCATTTGTAGGAATGGAAATAATAACAGTACATATTA… DONE
Testing specificity… DONE
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 952 Oligo selected
Updating thermodata… DONE
Folding CTCATAGTTTCTTATTGCTGGATAGGTACCTGTTTCTAAGCC… DONE
Testing specificity… DONE
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 909 Oligo selected
Updating thermodata… DONE
Folding ATGTAAGTGACACAAAGGCAGGAAATATAATTAAAAGGCTCT… DONE
Testing specificity… DONE
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 866 Oligo selected
Updating thermodata… DONE
Folding TTCCCCCTCTTCTAAGGGGAGGGCTTGGAAAGCAGTCATTAG… DONE
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 823 rejected due to a secondary structure (deltaG = -0.192 @ 76.0 degrees)
Updating thermodata… DONE
Folding ATTCCCCCTCTTCTAAGGGGAGGGCTTGGAAAGCAGTCATTA… DONE
Chr2:71387504-73101130centE0p1tocentE0p2_1360_pt1 822 rejected due to a secondary structure (deltaG = -0.192 @ 76.0 degrees)
Current Run:
Testing specificity… DONE
ENST00000000233P5_pt2 12 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding GGCCAGGTTGGGAGGGGGAAGGTGAGGGCT… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 11 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding GGGCCAGGTTGGGAGGGGGAAGGTGAGGGC… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 10 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding GGGGCCAGGTTGGGAGGGGGAAGGTGAGGG… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 9 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding AGGGGCCAGGTTGGGAGGGGGAAGGTGAGG… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 8 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding TAGGGGCCAGGTTGGGAGGGGGAAGGTGAG… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 7 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding CTAGGGGCCAGGTTGGGAGGGGGAAGGTGA… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 6 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding TCTAGGGGCCAGGTTGGGAGGGGGAAGGTG… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 5 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding CTCTAGGGGCCAGGTTGGGAGGGGGAAGGT… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 4 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding ACTCTAGGGGCCAGGTTGGGAGGGGGAAGG… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 3 Non specific oligo ignored at this time
Updating thermodata… DONE
Folding TACTCTAGGGGCCAGGTTGGGAGGGGGAAG… DONE
Testing specificity… DONE
ENST00000000233P5_pt2 2 Non specific oligo ignored at this time
Picking non specific oligos
ENST00000000233P5_pt2 74 Non specific oligos selected
ENST00000000233P5_pt2 43 Non specific oligos selected
ENST00000000233P5_pt2 12 Non specific oligos selected
More notes
- I think I have this working now building a BLAST fasta out of the modified names. Don’t see why this is necessary, doesn’t seem to have been essential previously.
- Now it lists multiple target hits in the _oligos.txt file as well as the name of the BLAST hit (these were previously blank).