CS3824
Fall, 2015
Course Project


Project Description (PDF)


Some Relevant Papers


Teams

Will be announced through email.


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
    


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