SNP2CAPS可将SNP转换为CAPS标记，其具体用法：

perl SNP2CAPS.pl   chr5D:9950377.fa_1    link_gcg    AanI,AarI,AasI,AatII,Aba6411II,AbaB8342IV,AbaCIII   > chr5D:9950377.txt

其中chr5D:9950377.fa_1为SNP两端各150bp的序列；link_gcg限制性内切酶数据库；之后为分析用到的限制性内切酶列表 ；chr5D:9950377.txt为输出文件

chr5D:9950377.fa_1示例：
>chr5D:9950377_Ref
ACAACTTTATCTCGTATTTCATAGCAGTAGCCAACCAATCTTATGATATTTTGATGTTGGGCCCTCATAAGATTCAGAAGCTCATTCTTAAAACCAGCTTCGACTAGTCCGGGCTGGTTGTACAGTTTCTTCACGGCAATCACTTCCCCGTTATCAAGTACTCCCTGTTCAAAATCCCATGTTTAAAAGTAATAATGCAAGGGTTCAGGTAGCTAGTGTAGTGGTGGCATCTGTTTAAAAGTATTATTTTTTTCGTAAAATGCGCTTAATTTTCCTCCCAGCAACCTTTCCACCAACTGAT
>chr5D:9950377_Alt
ACAACTTTATCTCGTATTTCATAGCAGTAGCCAACCAATCTTATGATATTTTGATGTTGGGCCCTCATAAGATTCAGAAGCTCATTCTTAAAACCAGCTTCGACTAGTCCGGGCTGGTTGTACAGTTTCTTCACGGCAATCACTTCCCCGCTATCAAGTACTCCCTGTTCAAAATCCCATGTTTAAAAGTAATAATGCAAGGGTTCAGGTAGCTAGTGTAGTGGTGGCATCTGTTTAAAAGTATTATTTTTTTCGTAAAATGCGCTTAATTTTCCTCCCAGCAACCTTTCCACCAACTGAT

link_gcg文件如果找不到，可在这下载：

链接：https://pan.baidu.com/s/1eJGIOs2O8cULYbAbc83JCA 密码：ru01

输出文件chr5D:9950377.txt示例：
#Marker Enzyme  Total size      Restriction Sites       Expected Fragments      Members

Predicted CAPS candidates
-------------------------

chr5D:9950377   AbaCIII 301     153     153,148 Alt
chr5D:9950377   AbaCIII 301             301     Ref

chr5D:9950377   AciI    301     148     153,148 Alt
chr5D:9950377   AciI    301             301     Ref

chr5D:9950377   BscGI   301             301     Alt
chr5D:9950377   BscGI   301     148     153,148 Ref

chr5D:9950377   BspACI  301     148     153,148 Alt
chr5D:9950377   BspACI  301             301     Ref

chr5D:9950377   FauI    301     155     155,146 Alt
chr5D:9950377   FauI    301             301     Ref

chr5D:9950377   LlaG50I 301     133     168,133 Alt
chr5D:9950377   LlaG50I 301     133,150 151,133,17      Ref

chr5D:9950377   SsiI    301     148     153,148 Alt
chr5D:9950377   SsiI    301             301     Ref


Following markers could not be converted into CAPS
--------------------------------------------------

如果输出文件很多，这里有脚本可以批量提取酶信息，脚本如下。

#!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Long;
use Config::General;
use Cwd qw(abs_path getcwd);
use FindBin qw($Bin $Script);
use File::Basename qw(basename dirname);
use Bio::SeqIO;
use Bio::Seq;
my $version = "1.3";
## prepare parameters #######################################################################
## -------------------------------------------------------------------------------------------
## GetOptions
my %opts;
GetOptions(\%opts, "id=s", "od=s", "h");
my $od = $opts{od};
$od = abs_path($od);
my $id = $opts{id};
$id = abs_path($id);
open(OUT,">$od/caps_out.txt") || die "open $od/caps_out.txt failed\n";
my @sample = glob ("$id/*.txt");
foreach my $i (@sample){
my $basename = basename ($i);
open(IN,"$i") || die "open $i failed\n";
while(<IN>){
next if(/^S2C#Format:/);
next if(/^#/);
next if(/^Predicted CAPS candidates/);
next if(/^-/);
next if(/^Following markers could not be converted into CAPS/);
next if(/^$/);
next if(!/\t/);
print OUT $_;
}
close(IN);
}
close(OUT);