Dataset formats

The input dataset is in tabular format and must contain a scaffold or chromosome column and a position column. The output dataset is in text format as described below. (Dataset missing?)

What it does

This tool extracts primers for SNPs in the dataset using the Primer3 program (Steve Rozen and Helen J. Skaletsky, 2000). The first line of output for a given SNP reports the name of the assembled contig, the SNP's position in the contig, the two variant nucleotides, and Primer3's "pair penalty". The next line, if not blank, names restriction enzymes (from the user-adjustable list) that differentially cut at that site, but do not cut at any other position between and including the primer positions. The next lines show the SNP's flanking regions, with the SNP position indicated by "n", including the primer positions and an additional 3 nucleotides.

Example

• input (gd_snp format):

  chr5_30800874_30802049    734   G  A  chr5   30801606   A  24  0  99   4  11  97   Y  496  0.502  0.033  0.215  6
  chr8_55117827_55119487    994   A  G  chr8   55118815   G  25  0  102  4  11  96   Y  22   0.502  0.025  2.365  1
  chr9_100484836_100485311  355   C  T  chr9   100485200  T  27  0  108  6  17  100  Y  190  0.512  0.880  2.733  4
  chr12_3635530_3637738     2101  T  C  chr12  3637630    T  25  0  102  4  13  93   Y  169  0.554  0.024  0.366  4
  etc.
  

• output:

  chr5_30800874_30802049 734 G A 0.352964
   BglII,MboI,Sau3AI,Tru9I,XhoII
    1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA
         >>>>>>>>>>>>>>>>>>>>
  
   61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT
  
  
   21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT
                                                           <<<<<<<
  
  181 TGAACCTTGGCTCTGA
      <<<<<<<<<<<<<
  etc.