# Last edited on 2017-02-11 11:30:46 by stolfilocal


Creating a dataset of real matches

ESCHERICHIA: EDH1 x E933

  In 2012, Rafael ran this program:

    lastz.v1.02.00 \
        bas/EDH1.bas \
        bas/E933.bas \
        --notrivial

  Parameters:
    
    EDH1 = /Escherichia_coli/ var K 12 DH1        4630707 bases
    E933 = /Escherichia_coli/ var O157 H7 EDL933  5521804 bases

  Scoring matrix:

         A    C    G    T
        91 -114  -31 -123
      -114  100 -125  -31
       -31 -125  100 -114
      -123  -31 -114   91
      O = 400, E = 30, K = 3000, L = 3000, M = 0
      
  The output was saved as lav/EDH1_E933_LASTZ.lav

DROSOPHILA: DSIM x DYAK

  The following sequences were downloaded from NCBI using FASTA (text) format:

    bas/CM000365.1.bas - Drosophila simulans chromosome 4, complete
    bas/CM000191.2.bas - Drosophila yakuba chromosome 4, complete
  
  In 2012, Rafael prepared these "normalized" files by removing all nucleotides
  except ATCG: 
  
    bas/DSIM.bas - from bas/CM000365.1.bas
    bas/DYAK.bas - from bas/CM000191.2.bas

  In 2012, Rafael ran this program:

    lastz.v1.02.00 DSIM.bas DYAK.bas --notrivial --identity=70..100

  Parameters:
    
    DSIM = /Drosophila simulans/  807946 bases
    DYAK = /Drosophila dyakuba/  1363842 bases

  Scoring matrix:
  
         A    C    G    T
        91 -114  -31 -123
      -114  100 -125  -31
       -31 -125  100 -114
      -123  -31 -114   91
      O = 400, E = 30, K = 3000, L = 3000, M = 0
      
  The output was saved as lav/DSIM_DYAK_LASTZ.lav
  
CONVERSION TO CDV FORMAT:

  Running {dm_lav_to_cdv}.  For each ".lav" file found with LASTZ, 
  create candidate files with 
    
    (a) all pairings, 
    (b) pairings with at least 2048 rungs and 85% matches
    (c) pairings with at least 256 rungs and 90% matches
   
    for tt in \
      DSIM:807946:DYAK:1363842:LASTZ:0:00 \
      DSIM:807946:DYAK:1363842:LASTZ:2048:85 \
      DSIM:807946:DYAK:1363842:LASTZ:256:90 \
      \
      EDH1:4630707:E933:5521804:LASTZ:0:00 \
      EDH1:4630707:E933:5521804:LASTZ:2048:85 \
      EDH1:4630707:E933:5521804:LASTZ:256:90 \
      ;
    do
      convert_lav_file.sh `echo ${tt} | tr ':' ' '` ;
    done
    ls -l cdv/*.cdv

  Got only the un-reversed matches; there were many reversed matches.
  
CREATING FALSE CANDIDATES

  Scrambling the 90% candidates to create false candidates:
  
    for tt in \
      DSIM:DYAK:LASTZ:2048:85 \
      EDH1:E933:LASTZ:2048:85 \
      ;
    do
      scramble_cands.sh `echo ${tt} | tr ':' ' '` ;
    done
    ls -l cdv/*_FF.cdv