CS3824
Fall, 2015
Course Project

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Project Description (PDF)

• Project Description (LaTeX)

• EmbedMotif.py

• RandomMotifFinder.py

• EvaluateLogLikelihood.py

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Some Relevant Papers

• Timothy L. Bailey and Charles Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization". Machine Learning 21, 51-80 (1995).

• Leping Li, "GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Couple with an EM Algorithm for Motif Discovery". Journal of Computational Biology 16, 317-329 (2009).

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Teams

Will be announced through email.

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Test Sequences

1. sequences_k2_d0_n100_m10_mu0.fasta and EmbedMotif_k2_d0_n100_m10_mu0.log
   Created by

   EmbedMotif.py -k 2 -d 0 -n 100 -m 10 --mu 0 sequences_k2_d0_n100_m10_mu0.fasta
   

2. sequences_k12_d3_n10_m100_mu0.10.fasta and EmbedMotif_k12_d3_n10_m100_mu0.10.log
   Created by

   EmbedMotif.py -k 12 -d 3 -n 10 -m 100 --mu 0.10 sequences_k12_d3_n10_m100_mu0.10.fasta
   

3. sequences_k13_d5_n20_m100_mu0.15.fasta and EmbedMotif_k13_d5_n20_m100_mu0.15.log
   Created by

   EmbedMotif.py -k 13 -d 5 -n 20 -m 100 --mu 0.15 sequences_k13_d5_n20_m100_mu0.15.fasta
   

4. sequences_k10_d2_n20_m120_mu0.10.fasta and EmbedMotif_k10_d2_n20_m120_mu0.10.log
   Created by

   EmbedMotif.py -k 10 -d 2 -n 20 -m 120 --mu 0.10 sequences_k10_d2_n20_m120_mu0.10.fasta
   

5. sequences_k12_d2_n40_m100_mu_0.10_a0.40_c0.10_g0.20.fasta and EmbedMotif_k12_d2_n40_m100_mu_0.10_a0.40_c0.10_g0.20.log
   Created by

   EmbedMotif.py -k 12 -d 2 -n 40 -m 100 --mu 0.10 -a 0.40 -c 0.10 -g 0.20 sequences_k12_d2_n40_m100_mu_0.10_a0.40_c0.10_g0.20.fasta
   

6. sequences_k13_d1_n40_m100_mu0.15.fasta and EmbedMotif_k13_d1_n40_m100_mu0.15.log
   Created by

   EmbedMotif.py -k 13 -d 1 -n 40 -m 100 --mu 0.15 sequences_k13_d1_n40_m100_mu0.15.fasta
   

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Project Performance

Every motif finder, including RandomMotifFinder, was given 100 seconds of execution time.

Team	Test Sequence 6; Run 1	Test Sequence 6; Run 2	Test Sequence 6; Run 3
Alpha	17.6337?	17.9908?	17.9574???
Beta	20.8404?	20.9782?	20.9872?
Gamma	19.9149	19.8608	20.3445
Delta	20.8950	20.8950	20.8950
Epsilon	19.8102	19.2767	18.5990
Optimal (Maybe?)	20.9861	20.9861	20.9861
RandomMotifFinder	8.0112	8.2642	7.8951

? Could not run EvaluateLogLikelihood on result

??? Log likelihood calculated by EvaluateLogLikelihood does not match

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