六框翻译六框翻译-⽣信⼈必练的200个数据处理任务-⽣信技能树 /thread-1444-1-1.html(出处: ⽣信技能树)密码⼦是按3个碱基翻译的，所以从第⼀位开始翻译会得到⼀个氨基酸序列，从第⼆位翻译会得到⼀个不同的氨基酸序列从第三位开始⼜会得到⼀个不同的序列。
从第四位开始就会和第⼀个开始翻译的序列⼀样（因为这两个都是从序列⾥⾯的起始密码⼦开始翻译的），所以相对于单链，会有3种翻译的⽅式，同样的情况在互补链上也会有3种，所以就⼀共有六种翻译⽅式。
读出六条序列，即6框翻译。
关于真核⽣物翻译的起始起始：⾸先是核糖体40s⼩亚基以及⼀些真核翻译起始因⼦结合mRNA的5'帽结构形成复合体，之后就会向下滑动，找AUG，翻译起始还要受到AUG附近序列控制，⽐如Kozak序列：CCa／gCCAUGG，如果找到了AUG，⽽且附近的序列⼜⽐较适合起始，那my(%codon) = ('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);$dna=shift@ARGV;$protein="";for(my$i=0; $i < (length($dna) - 2) ; $i += 3){$protein.=$codon{substr($dna,$i,3)} }print"+1\t$protein\n";$protein="";for(my$i=1; $i < (length($dna) - 2) ; $i += 3){$protein.=$codon{substr($dna,$i,3)} }print"+2\t$protein\n";$protein="";for(my$i=2; $i < (length($dna) - 2) ; $i += 3){$protein.=$codon{substr($dna,$i,3)} }print"+3\t$protein\n";$dna=reverse($dna);$dna=~tr/ACGTacgt/TGCAtgca/;$protein="";for(my$i=0; $i < (length($dna) - 2) ; $i += 3){$protein.=$codon{substr($dna,$i,3)} }print"-1\t$protein\n";$protein="";for(my$i=1; $i < (length($dna) - 2) ; $i += 3){$protein.=$codon{substr($dna,$i,3)} }print"-2\t$protein\n";$protein="";for(my$i=2; $i < (length($dna) - 2) ; $i += 3){$protein.=$codon{substr($dna,$i,3)} }print"-3\t$protein\n";注：还可以参照下⾯的代码1use strict;2use warnings;45my$dna ='';6my$protein ='';7my@file_data=( );8my@filedata;9my$revcom='';101112#打开⽂件13@filedata = get_file_data();14#得到序列15$dna = extract_sequence_from_fasta_data(@filedata);1617#六框阅读翻译1819print"\n---------------------Reading Frame 1-----------------\n";20$protein=translate_frame($dna,1);21 print_sequence($protein,70);2223print"\n---------------------Reading Frame 2-----------------\n";24$protein=translate_frame($dna,2);25 print_sequence($protein,70);2627print"\n---------------------Reading Frame 3-----------------\n";28$protein=translate_frame($dna,3);29 print_sequence($protein,70);3031print"\n---------------------Reading Frame 4-----------------\n";32$protein=translate_frame($dna,4);33 print_sequence($protein,70);3435print"\n---------------------Reading Frame 5-----------------\n";36$protein=translate_frame($dna,5);37 print_sequence($protein,70);3839print"\n---------------------Reading Frame 6-----------------\n";40$protein=translate_frame($dna,6);41 print_sequence($protein,70);4243sub get_file_data44 {45# A subroutine to get data from a file given its filename46 #读取⽂件的⼦序列47my$dna_filename;48my@filedata;49print"please input the Path just like this f:\\\\perl\\\\data.txt\n";50chomp($dna_filename=<STDIN>);51open(DNAFILENAME,$dna_filename)||die("can not open the file!");52@filedata = <DNAFILENAME>;53close DNAFILENAME;54return@filedata;#⼦函数的返回值⼀定要记住写55 }5657sub extract_sequence_from_fasta_data58 {59#*******************************************************************60 # A subroutine to extract FASTA sequence data from an array61 # 得到其中的序列62 # fasta格式介绍：63 # 包括三个部分64 # 1.第⼀⾏中以>开头的注释⾏，后⾯是名称和序列的来源65 # 2.标准单字母符号的序列66 # 3.*表⽰结尾67 #*******************************************************************6869my (@fasta_file_data) =@_;70my$sequence ='';71foreach my$line (@fasta_file_data)72 {73#这⾥忽略空⽩⾏74if ($line=~/^\s*$/)75 {76next;77 }78#忽略注释⾏79elsif($line=~/^\s*#/)80 {81next;82 }83#忽略fasta的第⼀⾏84elsif($line=~/^>/)85 {86next;87 }88else89 {90$sequence .=$line;91 }92 }93$sequence=~s/\s//g;94return$sequence;95 }9697sub print_sequence98 {99# A subroutine to format and print sequence data100my ($sequence, $length) = @_;101for (my$pos =0; $pos<length($sequence);$pos+=$length)102 {103print substr($sequence,$pos,$length),"\n";104 }105 }106107108109sub codon2aa110 {111112#第三种⽅法113 #也就是运⽤哈希114 #我们将所有的密码⼦作为hash的key，然后将代表的氨基酸作为hash的value 115 #然后进⾏匹配116 # codon2aa117 # A subroutine to translate a DNA 3-character codon to an amino acid118 # Version 3, using hash lookup119my($codon) = @_;120121$codon = uc$codon;#uc=uppercase;lc=lowercase122 #也就是⼤⼩写转换，uc表⽰将所有的⼩写转换为⼤写123 #lc将所有的⼤写转换为⼩写124125my(%genetic_code) = (127'TCA' => 'S', # Serine128'TCC' => 'S', # Serine129'TCG' => 'S', # Serine130'TCT' => 'S', # Serine131'TTC' => 'F', # Phenylalanine132'TTT' => 'F', # Phenylalanine133'TTA' => 'L', # Leucine134'TTG' => 'L', # Leucine135'TAC' => 'Y', # Tyrosine136'TAT' => 'Y', # Tyrosine137'TAA' => '_', # Stop138'TAG' => '_', # Stop139'TGC' => 'C', # Cysteine140'TGT' => 'C', # Cysteine141'TGA' => '_', # Stop142'TGG' => 'W', # Tryptophan143'CTA' => 'L', # Leucine144'CTC' => 'L', # Leucine145'CTG' => 'L', # Leucine146'CTT' => 'L', # Leucine147'CCA' => 'P', # Proline148'CCC' => 'P', # Proline149'CCG' => 'P', # Proline150'CCT' => 'P', # Proline151'CAC' => 'H', # Histidine152'CAT' => 'H', # Histidine153'CAA' => 'Q', # Glutamine154'CAG' => 'Q', # Glutamine155'CGA' => 'R', # Arginine156'CGC' => 'R', # Arginine157'CGG' => 'R', # Arginine158'CGT' => 'R', # Arginine159'ATA' => 'I', # Isoleucine160'ATC' => 'I', # Isoleucine161'ATT' => 'I', # Isoleucine162'ATG' => 'M', # Methionine163'ACA' => 'T', # Threonine164'ACC' => 'T', # Threonine165'ACG' => 'T', # Threonine166'ACT' => 'T', # Threonine167'AAC' => 'N', # Asparagine168'AAT' => 'N', # Asparagine169'AAA' => 'K', # Lysine170'AAG' => 'K', # Lysine171'AGC' => 'S', # Serine172'AGT' => 'S', # Serine173'AGA' => 'R', # Arginine174'AGG' => 'R', # Arginine175'GTA' => 'V', # Valine176'GTC' => 'V', # Valine177'GTG' => 'V', # Valine178'GTT' => 'V', # Valine179'GCA' => 'A', # Alanine180'GCC' => 'A', # Alanine181'GCG' => 'A', # Alanine182'GCT' => 'A', # Alanine183'GAC' => 'D', # Aspartic Acid184'GAT' => 'D', # Aspartic Acid185'GAA' => 'E', # Glutamic Acid186'GAG' => 'E', # Glutamic Acid187'GGA' => 'G', # Glycine188'GGC' => 'G', # Glycine189'GGG' => 'G', # Glycine190'GGT' => 'G', # Glycine191 );192193if(exists$genetic_code{$codon})194 {195return$genetic_code{$codon};196 }197else198 {199200print STDERR "Bad codon \"$codon\"!!\n";201exit;202 }203 }204205sub dna2peptide206 {207my ($dna)=@_;208my$protein ='';209for (my$i=0; $i<(length($dna)-2);$i+=3)210 {211$protein .=codon2aa(substr($dna,$i,3));212 }213return$protein;#这个词错误找了⼀晚上，没有返回值，所以结果总是没有内容，以后要引以为戒，⼦程序⼀定要有返回值214 }215216sub translate_frame217 {218my ($seq,$start,$end)=@_;219my$protein;220221unless($end)222 {223$end=length($seq);224 }225return dna2peptide(substr($seq,$start-1,$end-$start+1));226 }。
