• 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



  • CGPDB
    UC Davis


    Step 20: Usage of "Contig_Target" perl script and Primer3 program


    In UNIX shell following command has been executed. By "-x" option we specify file name with "target" info; "-a" option specifies tab-delimited file with consensus sequences.


    $ perl contig_target_May_01_2003.pl -x primer_picker.in -a tomato_ABC.fasta.cap.contigs.one_line.tab


    Output file "primer_picker.in.out" will be generated with detailed information about oligos (if found) for PCR. [Note, that for contig 1104 primers were not designed by Primer3 program. Manual selection in this case, probably, required].


    Finally, set up and enjoy PCR: