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Why N-SCAN Works Part 3 of 5,498. Bob Zimmermann 12/14/2005 (My 25th Birthday). Why Are We Concerned?. N-SCAN works just about as well in human with one informant as it does with eight.

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why n scan works part 3 of 5 498

Why N-SCAN WorksPart 3 of 5,498

Bob Zimmermann

12/14/2005

(My 25th Birthday)

why are we concerned
Why Are We Concerned?
  • N-SCAN works just about as well in human with one informant as it does with eight.
  • This means N-SCAN’s fancy phylogenetic mutation rate model has little effect on the outcome of the human predictions
  • Not always the case (fly).
what are we doing to find out what s going on
What Are We Doing to Find Out What’s Going On?
  • Take all the differences between N-SCAN and Twinscan and run them on both to compare the results
  • (Hopefully) discover that some additional information is coded in the conservation model that wasn’t there before
  • Eventually improve the conservation model
what s different
What’s Different
  • UTR States (Randy/Sam)
  • PSC “Magic Constant” (Rachel/Randy)
  • MultiZ alignments (Bob/Randy)
  • CNC State (Bob/Randy)
  • Independence Assumptions (Randy)
  • The Model Itself (Randy)

Could there be (gasp!) a bug?

multiz alignments
MultiZ Alignments
  • “Threaded Blockset Aligner”
  • Multiple alignments are usually done with a “reference sequence” -- not here
  • Constructed from pair BlastZ alignments
  • Reducing to Human-Mouse alignment should be nearly equivalent to pair BlastZ alignment
doesn t help
Doesn’t Help
  • Blast
  • Multiz

Gene Sensitivity 24.07%

Gene Specificity 12.44%

Transcript Sensitivity 21.32%

Transcript Specificity 12.44%

Exon Sensitivity 83.56%

Exon Specificity 34.91%

Nucleotide Sensitivity 89.83%

Nucleotide Specificity 44.08%

Gene Sensitivity 23.41%

Gene Specificity 9.51%

Transcript Sensitivity 20.74%

Transcript Specificity 9.51%

Exon Sensitivity 82.19%

Exon Specificity 32.66%

Nucleotide Sensitivity 88.72%

Nucleotide Specificity 41.73%

what s the cnc state1
What’s the CNC State?
  • In N-SCAN, prevents the 5’ UTR state from being entered too often
  • In theory, it should favor taking an OK-scoring CNC State over what should be a low-scoring CDS state visit.
  • Not really “trained” per se, just given the same conservation parameters as the 5’ UTR states
so what
So What?
  • This probably isn’t how N-Scan gets its boost. (Good.)
  • Perhaps the CNC state can be trained better.
  • More later….