perl应用：六框阅读翻译DNA序列
生物学知识：
1.六框翻译
因为DNA为双链, 平时从NCBI等里面得到的只是其中的一条链,还有一个互补链没有结出. 先从一条链讲起, 如此链为ACGATGCCG....则现在有以下三种读法：第一种，ACG/ATG/CCG.... 第二种，把A看做前面的部分，则为A/CGA/TGC/CG..... 第三种，把AC看做是前面的部分，则为AC/GAT/GCC/G... 只此一条链就有三种读码框。当然，互补链也有其对应的三个读码框，所以两者加起来是六个读码框了。
比如序列：ACGACGACGACGACGACG，可能的读码框就有以下三种:
ACG ACG ACG ACG ACG ACG ACG ACG
CGA CGA CGA CGA CGA CGA CGA CGA
GAC GAC GAC GAC GAC GAC GAC GAC
use strict; use warnings; my $dna =''; my $protein =''; my @file_data=( ); my @filedata;my $revcom='';#打开文件 @filedata = get_file_data();#得到序列$dna = extract_sequence_from_fasta_data(@filedata); #六框阅读翻译print "\n---------------------Reading Frame 1-----------------\n";$protein=translate_frame($dna,1);print_sequence($protein,70);print "\n---------------------Reading Frame 2-----------------\n";$protein=translate_frame($dna,2);print_sequence($protein,70);print "\n---------------------Reading Frame 3-----------------\n";$protein=translate_frame($dna,3);print_sequence($protein,70);print "\n---------------------Reading Frame 4-----------------\n";$protein=translate_frame($dna,4);print_sequence($protein,70);print "\n---------------------Reading Frame 5-----------------\n";$protein=translate_frame($dna,5);print_sequence($protein,70);print "\n---------------------Reading Frame 6-----------------\n";$protein=translate_frame($dna,6);print_sequence($protein,70);sub get_file_data{ # A subroutine to get data from a file given its filename#读取文件的子序列 my $dna_filename;my @filedata; print "please input the Path just like this f:\\\\perl\\\\data.txt\n"; chomp($dna_filename=<STDIN>); open(DNAFILENAME,$dna_filename)||die("can not open the file!"); @filedata = <DNAFILENAME>; close DNAFILENAME; return @filedata;#子函数的返回值一定要记住写}sub extract_sequence_from_fasta_data { #******************************************************************* # A subroutine to extract FASTA sequence data from an array # 得到其中的序列 # fasta格式介绍： # 包括三个部分 # 1.第一行中以>开头的注释行，后面是名称和序列的来源 # 2.标准单字母符号的序列 # 3.*表示结尾 #******************************************************************* my (@fasta_file_data) =@_; my $sequence =' '; foreach my $line (@fasta_file_data) { #这里忽略空白行 if ($line=~/^\s*$/) { next; } #忽略注释行 elsif($line=~/^\s*#/) { next; } #忽略fasta的第一行 elsif($line=~/^>/) { next; } else { $sequence .=$line; } } $sequence=~s/\s//g; return $sequence; } sub print_sequence { # A subroutine to format and print sequence data my ($sequence, $length) = @_; for (my $pos =0; $pos<length($sequence);$pos+=$length) { print substr($sequence,$pos,$length),"\n"; } } sub codon2aa { #第三种方法 #也就是运用哈希 #我们将所有的密码子作为hash的key，然后将代表的氨基酸作为hash的value #然后进行匹配 # codon2aa # A subroutine to translate a DNA 3-character codon to an amino acid # Version 3, using hash lookup my($codon) = @_; $codon = uc $codon;#uc=uppercase;lc=lowercase #也就是大小写转换，uc表示将所有的小写 转换为大写 #lc将所有的大写转换为小写 my(%genetic_code) = ( 'TCA' => 'S', # Serine 'TCC' => 'S', # Serine 'TCG' => 'S', # Serine 'TCT' => 'S', # Serine 'TTC' => 'F', # Phenylalanine 'TTT' => 'F', # Phenylalanine 'TTA' => 'L', # Leucine 'TTG' => 'L', # Leucine 'TAC' => 'Y', # Tyrosine 'TAT' => 'Y', # Tyrosine 'TAA' => '_', # Stop 'TAG' => '_', # Stop 'TGC' => 'C', # Cysteine 'TGT' => 'C', # Cysteine 'TGA' => '_', # Stop 'TGG' => 'W', # Tryptophan 'CTA' => 'L', # Leucine 'CTC' => 'L', # Leucine 'CTG' => 'L', # Leucine 'CTT' => 'L', # Leucine 'CCA' => 'P', # Proline 'CCC' => 'P', # Proline 'CCG' => 'P', # Proline 'CCT' => 'P', # Proline 'CAC' => 'H', # Histidine 'CAT' => 'H', # Histidine 'CAA' => 'Q', # Glutamine 'CAG' => 'Q', # Glutamine 'CGA' => 'R', # Arginine 'CGC' => 'R', # Arginine 'CGG' => 'R', # Arginine 'CGT' => 'R', # Arginine 'ATA' => 'I', # Isoleucine 'ATC' => 'I', # Isoleucine 'ATT' => 'I', # Isoleucine 'ATG' => 'M', # Methionine 'ACA' => 'T', # Threonine 'ACC' => 'T', # Threonine 'ACG' => 'T', # Threonine 'ACT' => 'T', # Threonine 'AAC' => 'N', # Asparagine 'AAT' => 'N', # Asparagine 'AAA' => 'K', # Lysine 'AAG' => 'K', # Lysine 'AGC' => 'S', # Serine 'AGT' => 'S', # Serine 'AGA' => 'R', # Arginine 'AGG' => 'R', # Arginine 'GTA' => 'V', # Valine 'GTC' => 'V', # Valine 'GTG' => 'V', # Valine 'GTT' => 'V', # Valine 'GCA' => 'A', # Alanine 'GCC' => 'A', # Alanine 'GCG' => 'A', # Alanine 'GCT' => 'A', # Alanine 'GAC' => 'D', # Aspartic Acid 'GAT' => 'D', # Aspartic Acid 'GAA' => 'E', # Glutamic Acid 'GAG' => 'E', # Glutamic Acid 'GGA' => 'G', # Glycine 'GGC' => 'G', # Glycine 'GGG' => 'G', # Glycine 'GGT' => 'G', # Glycine ); if(exists $genetic_code{$codon}) { return $genetic_code{$codon}; } else { print STDERR "Bad codon \"$codon\"!!\n"; exit; } } sub dna2peptide { my ($dna)=@_; my $protein =''; for (my $i=0; $i<(length($dna)-2);$i+=3) { $protein .=codon2aa(substr($dna,$i,3)); } return $protein;#这个词错误找了一晚上，没有返回值，所以结果总是没有内容，以后要引以为戒，子程序一定要有返回值 } sub translate_frame{my ($seq,$start,$end)=@_;my $protein;unless($end){$end=length($seq);}return dna2peptide(substr($seq,$start-1,$end-$start+1));}