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PROGRAM TO STORE A DNA SEQUENCE
Aim To write a program to store a DNA sequence.
Program $dna="ATGC"; print"The DNA sequence is $dna";
Output The DNA sequence is ATGC
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PROGRAM TO CONCATENATE DNA FRAGMENTS
Aim To write a program to concatenate DNA fragments.
Program $DNA1="GTACAAAAAAGCAGAAGGGCCGTCA"; $DNA2="TACTTGGATGACTGTCACCGGAGGT"; $DNA3="TCATCTCCAAGTCCTTCCAGGGCAG"; $DNA=$d1.$d2.$d3; print"The Concatenated DNA Sequence is \n$DNA";
Output The Concatenated DNA Sequence is GTACAAAAAAGCAGAAGGGCCGTCATACTTGGATGACTGTCACCGGGGTTCA TCTCCAAGTCCTTCCAGGGCAG
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PROGRAM TO CONVERT DNA TO RNA SEQUENCE
Aim To write a program to convert DNA to RNA sequence.
Program $dna="CGAGCACTGTTTCCAACAAAAATCTAGGATCTTGGCAGTAACCACTAT; print"The DNA sequence is :\n\t$dna"; $com=$dna; $com=~s/T/U/g; print" The Converted RNA sequence is :\n\t$com";
Output The DNA sequence is : CGAGCACTGTTTCCAACAAAAATCTAGGATCTTGGCAGTAACCACTAT The converted RNA sequence is : CGAGCACUGUUUCCAACAAAAAUCUAGGAUCUUGGCAGUAACCACU
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PROGRAM TO CALCULATE REVERSE COMPLEMENT OF A DNA SEQUENCE
Aim To write a program to calculate reverse complement of a DNA sequence.
Program $dna="ATGCGTA"; print" the Dna sequence = $dna\n"; $reverse=reverse $dna; print"Reversed Dna sequence = $reverse\n"; $reverse=~tr/ATGC/TACG/; print"Reverse complement of Dna = $rev";
Output: The Dna sequence = ATGCGTA Reversed Dna sequence = ATGCGTA Reverse complement of Dna = TACGCAT
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PROGRAM TO READ PROTEIN SEQUENCE DATA FROM A FILE.
Aim: To write a program to read protein sequence data from a file.
Program: #!usr/bin/perl print"Enter the file name:"; $proteinfilename=
; open(PROTEINFILE,$proteinfilename); @protein=; print"@protein"; #close PROTEINFILE; #exit;
Output: Enter the file name: x:\cat.txt ATGTTCCACTTTATTGTTAACCCAAGTAGTCAAAGCGGAAAAAGCAAATCTCT CTGGAAGCTTATTGAGAGGGAACTAAA GGAGCACCACATCGATTATAAAGTCCACTACACTCGCTATGAGTACCATGCA ATCCAACTTGTCCAAGAGATCTGTAAGG AAAAAGGTTTTAAGACCATCGTTGCACTTGGAGGTGATGGAACCGTTAGTGA GGTAGTTAACGGAATTACAGACTTCGAT AATGTTAAATTTGGTTACATCCCAACAGGGTCAAGTAACGACTTCTCACGTGG TTTAGGACTTCCCACTAAGTTTAAGAA GGCCTTGGATACAGTTTTGTACTCTAAGAATTACAAAGAAATCGATGTTGGCT GCCTTGACTTTGGAAACAACGAAACAC AAAAATTCGGTGTTTCATGCGGCATGGGATTTGACGCTGCCGTTTGCATGGAA GCCTACTCATCACCCATCAAAGACTTC TTAAATCGTATCCATATGGGCTTTTTCACATATACTGTAATCGCAGTCAAGAA CATTTTTACTTACAAGTGTTCTAAGAT
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CACCATTACATTCGATGATAAGGATACACGCGTTTATGACCGTTGCCTCTTCC TTTCATCACTTAATGGCCCATGTGAAG GTGGTGGCTTGCGCCTTGCTCCACATGCTAACCCATTCGATGAATATCTCGAT GTGTTCGTTCTGAATACAGATAATAAG GTCAAGATTTTATTATTCTTCCCCTTAGCTTATCTGAATTGTCATAGTGCCCTT AACTACTTCGATGAAGTTGATATTGT AAGATGCAAGAAGCTTCACATTGTCTCAGACGTACCTCTTCCTGTCCACAGAG ATGGCGAACCATGCAAATACCGCACAG ATGTTACAATCTCACTTCAAAAGAAGAAGCTCAAAGTTTGCACACCATA
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PROGRAM TO PRINT THE ELEMENTS OF AN ARRAY
Aim To write a program to print the elements of an array.
Program @array=("ATGC","ACTG"); print"Elements of an array = @array";
Output Elements of an array = ATGC ACTG
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PROGRAM TO TAKE AN ELEMENT OFF THE END OF AN ARRAY
Aim To write a program to take an element off the end of an array.
Program @location=(1,2,3,4); print"The elements of an array is @location\n "; $num=pop@location; print"The removed end element of an array is $num\n"; print"The remaining array elements @location";
Output The elements of an array is 1 2 3 4 The removed end element of an array is 4 The remaining array elements 1 2 3
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PROGRAM TO TAKE AN ELEMENT OFF THE BEGINNING OF AN ARRAY
Aim To write a program to take an element off the beginning of an array.
Program @num=(1,2,3,4); print" The elements of an array is @num\n"; $num=shift@num; print" The removed beginning element of an array is $num\n"; print" The remaining array elements @num";
Output The elements of an array is 1 2 3 4 The removed beginning element of an array is 1 The remaining array elements 2 3 4
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PROGRAM TO PUT AN ELEMENT AT THE BEGINNING OF AN ARRAY.
Aim To write a program to put an element at the beginning of an array.
Program @num=(2,3); print" The elements of an array is @num\n"; $val=unshift @num,1; print"Inserted element is 1\n"; print" The array with inserted first element is @num\n";
Output The elements of an array is 2 3 Inserted element is 1 The array with inserted first element is 1 2 3
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PROGRAM TO PUT AN ELEMENT AT THE END OF AN ARRAY
Aim To write a program to put an element at the end of an array.
Program @char=("a","b","c"); print" The elements of an array is @char\n"; push@char,"d"; print" The inserted element is d\n"; print" The array with inserted end element is @char";
Output The elements of an array is a b c The inserted element is d The array with inserted first element is a b c d
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ADD AN ELEMENT TO THE BEGINING
Aim To write a perl program to put an element at the end of the array Program For string: @string= (“AB”,”CD”,”EF”); print “The array before adding is @string; @string1=”FA”; unshift @string,@string1; print “The array after adding is @string”; For numbers: @num= (1, 2, 3, 4, 5); print “The array before adding is @num; @num1=0; unshift @num,@num 1; print “The array after adding is @num”; Output The array before adding is ABCDEF The array after adding is FAABCDEF The array before adding is 12345 The array after adding is 012345
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PROGRAM TO REVERSE AN ARRAY
Aim To write a program to reverse an array.
Program @num=(1,2,3); print"The array in order is @num"; @rev=reverse @num; print"The array in reversed order @rev";
Output The array in order is 1 2 3 The array in reversed order 3 2 1
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PROGRAM TO GET THE LENGTH OF AN ARRAY
Aim To write a program to get the length of an array.
Program @Rollno=(1,2,3,4,5,6); print"The array is @ Rollno "; $students=scalar@Rollno; print"The length of an array = $students";
Output The array is 1 2 3 4 5 6 The length of an array = 6
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PROGRAM TO INSERT AN ELEMENT AT A RANDOM POSITION IN AN ARRAY
Aim To write a program to insert an element at a random position in an array.
Program @dna=('a','t','g','c'); print"The array is "; print"@dna\n"; splice(@dna,2,0,'x'); print"The spliced array is "; print"@dna";
Output The array is a t g c The spliced array is a t x g c
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PROGRAM TO FIND MOTIFS IN A PROTEIN SEQUENCE
Aim To write a program to find motifs in a protein sequence.
Program print"Enter the file name: "; $proteinfile=; chomp $proteinfile; open(PROTEINFILE,$proteinfile); @protein=; $protein=join('',@protein); print"Enter a motif to be searched for: "; $motif=; chomp$motif; if($protein=~/$motif/) { print"The pattern matched is found"; } else { print"The pattern not found"; }
Output Enter the file name: x:\insilico\catalase.txt Enter a motif to be searched for: AGLLW The pattern matched is found
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PROGRAM TO COUNT NUCLEOTIDES IN A SEQUENCE
Aim To write a program to count nucleotides in a sequence.
Program print"Enter the file name: "; $dnafile=; open(DNAFILE,$dnafile); @dna=; $dna=join('',@dna); @dna=split('',$dna); $A=0; $T=0; $G=0; $C=0; foreach $base(@dna) { if($base eq 'A') { $A++; } elsif($base eq 'T') { ++$T; } elsif($base eq 'G') { ++$G; } elsif($base eq 'C')
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print"Number of Adenine =$A\n"; print"Number of Thymine =$T\n"; Print”Number of Guanine =$G\n"; print"Number of Cytosine =$C\n";
Output Enter the file name: x:\insilico\rat.txt
-----------------------------------------------------------Number of Adenine =40 Number of Thymine =73 Number of Guanine =68 Number of Cytosine =54
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PROGRAM TO FIND THE PERCENTAGE OF HYDROPHOBIC AMINO ACIDS IN A SEQUENCE
Aim To write a program to find the percentage of hydrophobic amino acids in a sequence.
Program print"Enter the file name: "; $pro=; chomp $pro; open(PROTEINFILE,$pro); @ptn=; $ptn=join('',@ptn); $lenprotein=length$ptn; @ptn=split('',$ptn); $count_v=0; { foreach $base(@ptn) { if(($base eq 'V')||($base eq 'I')||($base eq 'F')||($base eq 'L')||($base eq 'M')||($base eq 'W')||($base eq 'C')) { ++$count_V; } } } print"\nLength of protein: $lenprotein"; print"\nHydrophobic amino acids=$count_V"; $per_V=($count_V/$lenprotein)*100; print"\nThe percentage of hydrophobic amino acid is $per_V";
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Enter the file name: x:\catalase.txt Length of protein: 499 Hydrophobic amino acids=141 The percentage of hydrophobic amino acid is 28.2565130260521
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PROGRAM TO APPEND ATGC TO A DNA SEQUENCE USING SUBROUTINES
Aim To write a program to append ATGC to a DNA sequence using subroutines.
Program sub append { $a='ATGC'; $res=$_[0]; $res=$res,$a; } $dna="TTAGTAAT"; print"The DNA sequence is: $dna"; $rna="UAGAAGCG"; print"\nThe RNA sequence is: $rna"; append $dna.$rna; print"\nAfter doing append the sequence is: $res";
Output The DNA sequence is: TTAGTAAT The RNA sequence is: UAGAAGCG After doing append the sequence is: TTAGTAATUAGAAGCG
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PROGRAM TO CONCATENATE TWO STRINGS USING SUBROUTINES
Aim To write a program to concatenate two strings using subroutines.
Program $DNA1='ATTATAAT'; print"The first sequence is $DNA1\n"; $DNA2='GCATTCAT'; print"The second sequence is $DNA2\n"; $DNA3=concat($DNA1,$DNA2); print"The concatenated sequence is $DNA3"; sub concat { $DNA3=$DNA1.$DNA2; return $DNA3; } Output The first sequence is ATTATAAT The second sequence is GCATTCAT The concatenated sequence is ATTATAATGCATTCAT
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PROGRAM TO CONVERT DNA TO RNA USING SUBROUTINES
Aim To write a program to convert DNA to RNA using subroutines.
Program $DNA='ATGACCGCTA'; print"The DNA sequence is $DNA"; $res=convert($DNA); print"\nThe RNA sequence is $res"; sub convert { $res=$DNA; $res=~s/T/U/g; return $res; } Output The DNA sequence is ATGACCGCTA The RNA sequence is AUGACCGCUA
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PROGRAM TO FIND IF A DNA IS STABLE OR NOT
Aim To write a program to find if a DNA is stable or not.
Program print"Enter the file name: "; $dna=; chomp $dna; open(DNAfile,$dna); @dna=; $joindna=join('',@dna); $lendna=length $joindna; @dnafinal=split('',$joindna); $count_A=0; $count_T=0; $count_G=0; $count_C=0; { foreach $base(@dnafinal) { if($base eq 'A') { ++$count_A; } elsif($base eq 'T') { ++$count_T; } elsif($base eq 'G') {
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print"The length of the dna is $lendna"; print"\nA=$count_A"; print"\nT=$count_T"; print"\nG=$count_G"; print"\nC=$count_C"; $count_AT=$count_A+$count_T; $count_GC=$count_G+$count_C; $per_AT=($count_AT/$lendna)*100; $per_GC=($count_GC/$lendna)*100; print"\nThe length of AT is $count_AT"; print"\nThe length of GC is $count_GC"; print"\nThe percentage of AT is $per_AT"; print"\nThe percentage of GC is $per_GC"; if($per_GC>$per_AT) { print"\nThe dna is stable"; } else { print"\nThe dna is not stable"; } } Output Enter the file name: x:\insilico\cat.txt
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The length of the dna is 229 A=59 T=39 G=63 C=68 The length of AT is 98 The length of GC is 131 The percentage of AT is 32.8859060402685 The percentage of GC is 43.9597315436242 The dna is stable
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PROGRAM TO FIND THE MOTIFS
Aim To write a program to find the motifs in a protein sequence
Program print"Enter the file name:"; $proteinfile=; open(PROTEINFILE,$proteinfile); @protein=; $joinprot=join('',@protein); $lenprotein=length$joinprot; print"Enter a motif:"; $motif=; chomp$motif; $lenmotif=length$motif; $count=0; for($position=0;$position<$lenprotein;++$position) { $motsearch=($joinprot) if($motsearch eq $motif); { ++$count; } } print"The number of motif=$count";
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Enter the file name: x:\nuc1.txt Enter a motif: GCATGTACTGTAC The number of motifs=528
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PROGRAM TO FIND THE PERCENTAGE OF G AND C
Aim To write a program to find the percentage of G and C in a given dna sequence
Program print"Enter your file containing DNA sequence "; $dnafile=; open(DNAFILE,$dnafile); @dna=; $dna=join('',@dna); @dna=split('',$dna); $GC=0; $length=scalar@dna; foreach $dna(@dna) { if(($dna eq'G')||($dna eq'C')) { $GC++; } } print"The total length of the sequence is $length\n"; print"The total number of G and C present is $GC\n"; $GC1=($GC/$length)*100; print"The percentage of G and C is $GC1\n";
Output Enter your file containing DNA sequence x:\nuc1.txt
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The total length of the sequence is 528 The total number of G and C present is 106 The percentage of G and C is 20.0757575757576
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PROGRAM TO CONVERT DNA TO PROTEIN SEQUENCE
Aim To write a program to convert dna to protein sequence Program print "This script will convert your DNA sequence to PROTEIN Sequence\n\n"; print "ENTER THE FILENAME OF THE DNA SEQUENCE:= "; $DNAfilename = ; chomp $DNAfilename; unless ( open(DNAFILE, $DNAfilename) ) { print "Cannot open file \"$DNAfilename\"\n\n"; } @DNA = ; close DNAFILE; $DNA = join( '', @DNA); print " \nThe original DNA file is:\n$DNA \n"; $DNA =~ s/\s//g; my $protein=''; my $codon; for(my $i=0;$i<(length($DNA)-2);$i+=3) { $codon=substr($DNA,$i,3); $protein.=&codon2aa($codon); } print "The translated protein is :\n$protein\n"; ;
sub codon2aa{ my($codon)=@_; $codon=uc $codon;
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my(%g)=('TCA'=>'S','TCC'=>'S','TCG'=>'S','TCT'=>'S','TTC'=>'F','TTT'=>'F','TTA'=>'L ','TTG'=>'L','TAC'=>'Y','TAT'=>'Y','TAA'=>'_','TAG'=>'_','TGC'=>'C','TGT'=>'C','TGA' =>'_','TGG'=>'W','CTA'=>'L','CTC'=>'L','CTG'=>'L','CTT'=>'L','CCA'=>'P','CCC'=>'P',' CCG'=>'P','CCT'=>'P','CAC'=>'H','CAT'=>'H','CAA'=>'Q','CAG'=>'Q','CGA'=>'R','CGC' =>'R','CGG'=>'R','CGT'=>'R','ATA'=>'I','ATC'=>'I','ATT'=>'I','ATG'=>'M','ACA'=>'T',' ACC'=>'T','ACG'=>'T','ACT'=>'T','AAC'=>'N','AAT'=>'N','AAA'=>'K','AAG'=>'K','AG C'=>'S','AGT'=>'S','AGA'=>'R','AGG'=>'R','GTA'=>'V','GTC'=>'V','GTG'=>'V','GTT'=>' V','GCA'=>'A','GCC'=>'A','GCG'=>'A','GCT'=>'A','GAC'=>'D','GAT'=>'D','GAA'=>'E',' GAG'=>'E','GGA'=>'G','GGC'=>'G','GGG'=>'G','GGT'=>'G'); if(exists $g{$codon}) { return $g{$codon}; } else { print STDERR "Bad codon \"$codon\"!!\n"; exit; } }
Output This script will convert your DNA sequence to PROTEIN Sequence
ENTER THE FILENAME OF THE DNA SEQUENCE: = x:\nuc.txt
The original DNA file is: TTAAATTCTAATTAGAGATGCAGGAATCAATGATAGGGAGGTTGGACAGCTC AGTTCCCCAGTGCCAGCC CAATAGACGGATGAGTTATTGTCATGTAAAAAGCGCCAGCAATAAGACCAAC CGCTTTGCTATTGTCCAA
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GTGGAAAGAGCCAAGTTTATTATGAGGACTATATGCTCTAGAGACCTCAGAC AAGGCATCTCATAGGAGG CTTTTTCATAAAACTAGGCTCTGCTGGTAGTAAGGAGGCCAGTTTGGAGGCA GGCGTTGAGCTGTGCACA TCTCCCCACTCCAGCCACCTTCTCCATATCCATCTTTTATTTCATTTTTCCACTT GGCTGAGCCATCCAG AACCTTTTCAATGTATAAAATGGAATATTCTTACCTCAATTCCTCTGCCTACG AGTCCTGTATGGCTGGG ATGGACACCTCGAGCCTGGCTTCAGCCTATGCTGACTTCAGTTCCTGCAGCCA GGCCAGTGGCTTCCAGT ATAACCCGATAAGGACCACTTTTGGGGCCACGTCCGGCTGCCCTTCCCTCACG CCGGGATCCTGCAGCCT GGGCACCCTCAGGGACCACCAGAGCAGTCCGTACGCCGCAGTTCCTTACAAA CTCTTCACGGACCACGGC GGCCTCAACGAGAAGCGCAAGCAGCGGCGCATCCGCACCACTTTCACCAGTG CCCAGCTCAAAGAGCTGG AAAGGGTCTTCGCGGAGACTCACTACCCCGACATCTACACTCGGGAGGAGCT GGCCCTGAAGATCGACCT CACAGAGGCGCGAGTCCAGGTGTGGTTCCAGAACCGCCGCGCCAAGTTTCGC AAGCAGGAGCGCGCAGCG GCAGCCGCAGCGGCCGCGGCCAAGAACGGCTCCTCGGGCAAAAAGTCTGAC TCTTCCAGGGACGACGAGA GCAAAGAGGCCAAGAGCACTGACCCGGACAGCACTGGGGGCCCAGGTCCCA ATCCCAACCCCACCCCCAG CTGCGGGGCGAATGGAGGCGGCGGCGGCGGGCCCAGCCCGGCTGGAGCTCC GGGGGCGGCGGGGCCCGGG GGCCCGGGAGGCGAACCCGGCAAGGGCGGCGCAGCAGCAGCGGCGGCGGCC GCGGCAGCGGCGGCGGCGG CAGCGGCAGCGGCGGCAGCTGGAGGCCTGGCTGCGGCTGGGGGCCCTGGAC AAGGCTGGGCTCCCGGCCC
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GTCTCATGTTTCGCAACTCTTTTTTTCCCCCTCGCTCCCGCCTACCCCGTCGGC ATTTTCTTCTTCCACC AGCTTTTACTGAACTTTTTGGCACTGCTTTGGATTGGGGTCAATTGCAGTCCA CGTAACTGGCTGCAGAG AAATCTACCGAGCAAGGAAAAGGCACACACACACGTTTGCAGGGGTGTCTCG GTTTGCATTTCTGTTGGA ATGATCCGAACTGGACTCACATCCTGTATGGTGGATGGACTGTATATTGAGG GTTCCATTCTTCGCGCAG TTTAGACATCTCTGTTTTGATTCTTTGTTGTTGTTTTTATTTTAAAAGGCACAA ACTCTAGATATTAGTT GAATGTTGAGGCTTTAACTTTTTCGGTGTCTTTCTACAACTGTGTTCTGTGACT CAATTGTATCGTGTTA The translated protein is: LNSN_RCRNQ__GGWTAQFPSASPIDG_VIVM_KAPAIRPTALLLSKWKEPSLL_G LYALETSDKASHRRLFHKTRLCW_ _GGQFGGRR_AVHISPLQPPSPYPSFISFFHLAEPSRTFSMYKMEYSYLNSSAYESC MAGMDTSSLASAYADFSSCSQAS GFQYNPIRTTFGATSGCPSLTPGSCSLGTLRDHQSSPYAAVPYKLFTDHGGLNEK RKQRRIRTTFTSAQLKELERVFAET HYPDIYTREELALKIDLTEARVQVWFQNRRAKFRKQERAAAAAAAAAKNGSSG KKSDSSRDDESKEAKSTDPDSTGGPGP NPNPTPSCGANGGGGGGPSPAGAPGAAGPGGPGGEPGKGGAAAAAAAAAAAA AAAAAAAAGGLAAAGGPGQGWAPGPGPI TSIPDSLGGPFASVLSSLQRPNGAKAALVKSSMF_SGILRRRRRRRQRASQGPGGR VGERVGPRLLSSLLPWLFH_GPKV IALRIKGKRRRPHFNPTPTPFLNPQTKQTNFPGFAPAWGLAAGPGLRLLIGGCEQR GLDAGHSQGAVSACQFVSVSGNVC LWPKQVTGRDGGPQPT__LV_KKKTKK_K_KQKSWKAETIKKQKANNPERFKKH KEKKDKLKEGLGEKLQLELKARSCEP LNPLPPNSTDSLGALLQGRVGTPFQPPFLSCPWVRVTAATTCSDCPGGRSDFLAP PCLSHLAEHHPAISASEPHTVATPN
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PESLQPFGPERCPIHEMPFHLQTLQNVSHVSQLFFSPSLPPTPSAFSSSTSFY_TFWH CFGLGSIAVHVTGCREIYRARK RHTHTFAGVSRFAFLLE_SELDSHPVWWMDCILRVPFFAQFRHLCFDSLLLFLF_K AQTLDIS_MLRL_LFRCLSTTVFC DSIVSC_YQCRLSPLRDRIMFFSSCSLYGVSLWCNKVLTGSIFCV_RGHGSDNGIY FCYQVHVCLISFFFLLDYVCEHNC HKLCFRFLNLFICVIMNASI_KGNISTCAYSFPRVYH_LDC___KQKASLK
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