• Intro

  • step_01
  • step_02
  • step_03
  • step_04
  • step_05
  • step_06
  • step_07
  • step_08
  • step_09
  • step_10
  • step_11
  • step_12
  • step_13
  • step_14
  • step_15
  • step_16
  • step_17
  • step_18
  • step_19
  • step_20
  • step_21
  • step_22
  • step_23
  • step_24

  • Credits

    UC Davis

    Step 11: Processing of the "Alignment Files" and
    finding all mismatches in ESTs versus consensus sequences

    At this step we have used Python_CAP3_MM_Finder_Feb_27_2004.py script to find all mismatches in ESTs versus consensus sequences.

    We need to change working directory to "tomato_alignments" and combine all "Alignment Files" into one file "L_ABC_Contigs_All.aln" using UNIX cat.

    $ cd tomato_alignments

    $ cat L_ABC_Contig* > L_ABC_Contigs_All.aln

    Execute Python_CAP3_MM_Finder_Feb_27_2004.py script in that directory. Example dialog is shown below:

    $ python Python_CAP3_MM_Finder_Feb_27_2004.py
    Enter the SOURCE file name: L_ABC_Contigs_All.aln
    Enter the DESTINATION file name: L_ABC_Contigs_All.aln.MM

    L_ABC_Contigs_All.aln.MM file will be generated containing information about all polymorphic sites. Example lines for the Contig1049 are shown below. "D" is deletion, "I" - insertion, "S" - substitution. Compare this information for position "72" [red dot] to the alignment in the previous step.