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<p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;">This program aims to <strong>demonstrate a few salient features of DNA</strong> got from a file. We first store the file name in a scalar variable $DNA. We open the file and read the first line of the file and store it $DNA2. As it is scalar it holds only one value at a time and hence the other lines of the file cannot be stored. We again open the same file but this time store the contents of the file in an array so that all the contents can be read and stored as values of the array @DNA.</span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;"> </span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;">We do a <strong>chomp</strong> on the array (@DNA) to remove the “enter” character. The “<strong>chop</strong>” command is used to remove the last character of a particular value. We demonstrate here the use of chop. When we use chop on the array @DNA (line 16), the last character of each value of the array is deleted or removed.</span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;"><span> </span></span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;">We use the <strong>“join”</strong> command to make one complete string of DNA from the array values. In line 22, a complementary of the DNA string ($DNA3) is got by translating A to T, C to G, G to C and T to A and saved again in $DNA3. A point to note here is that the translation works only letter by letter and not with words. We then again translate T to U to get the RNA. We now find the length of RNA by using the command called “length”. We then find out the total number of bases or nucleotides in the string by calculating the number of occurrences occurred while translating each of the nucleotides to a null value (see line 31 to 34) and totaling all the individual values.</span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;"><span> </span></span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;">We find out the GC percentage by calculating the number of occurrences while substituting the GC with itself, dividing it by total and multiplying it by 100. We substitute it by itself as we do not want to disturb the DNA structure but would want to know how many GCs are present. The number of adenines are already calculated in the line 31 we just do a copy to $A. We then use the substitute command to substitute the AUG and UAG to start and stop respectively.</span> </p> <p style="text-align:justify;"> <span style="font-size:10pt;font-family:Arial;"> </span> </p> <ol style="margin-top:0in;"><li><span style="font-size:10pt;font-family:'Courier New';">#<strong>file handler for single strand</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA="sample.seq";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">open (FILE,$DNA);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA2=<FILE>;</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">close FILE;</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the sequence of single strand of DNA:$DNA2\n";</span></li> <li><strong><span style="font-size:10pt;font-family:'Courier New';">#file handler for multiple strands of DNA</span></strong></li> <li><span style="font-size:10pt;font-family:'Courier New';">open (FILE,$DNA); </span></li> <li><span style="font-size:10pt;font-family:'Courier New';">@DNA=<FILE>;</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">close FILE;</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the sequences of multiple strands of DNA:@DNA\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>Chomp the multiple strands of DNA'</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">chomp (@DNA);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the result of chomp:@DNA\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>chop the<span> </span>sequences</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">chop (@DNA);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the result of chop function:@DNA\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>join the two strands</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA3=join('',@DNA);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the result of join:$DNA3\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>substitute for making a complementary copy of the joined strand</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA3=~(tr/ACGT/TGCA/);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the complementary result:$DNA3\n";</span></li> <li><strong><span style="font-size:10pt;font-family:'Courier New';">#to make a transcribed copy of the string</span></strong></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA3=~(tr/T/U/);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the transcribed RNA:$DNA3\n";</span></li> <li><strong><span style="font-size:10pt;font-family:'Courier New';">#total length of RNA</span></strong></li> <li><span style="font-size:10pt;font-family:'Courier New';">$length=length($DNA3);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the length of RNA:$length\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>total number of nucleotides</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$a=($DNA3=~tr/A//);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$b=($DNA3=~tr/C//);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$c=($DNA3=~tr/G//);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$d=($DNA3=~tr/U//);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$Total=$a+$b+$c+$d;</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the total nucleotides:in RNA:$Total\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>percent GC count</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$GCcount=($DNA3=~s/GC/GC/g);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the total number of GC in DNA :$GCcount:\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$GCper=($GCcount/($Total)*100);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the GC percentage:$GCper\n";</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">#<strong>number of A</strong></span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$A=($a);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the total number of Adenines:$A\n";</span></li> <li><strong><span style="font-size:10pt;font-family:'Courier New';">#substitute the start and stop codons</span></strong></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA3=~(s/AUG/start/g);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">$DNA3=~(s/UAG/Stop/g);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the start and stop codon:$DNA3\n";</span></li> <li><strong><span style="font-size:10pt;font-family:'Courier New';">#chop the terminal nucleotide of RNA</span></strong></li> <li><span style="font-size:10pt;font-family:'Courier New';">chop ($DNA3);</span></li> <li><span style="font-size:10pt;font-family:'Courier New';">print"the result of chop:$DNA3\n"; </span></li> <li><span style="font-size:10pt;font-family:'Courier New';">exit;</span></li> </ol><p> <span style="font-size:10pt;font-family:'Courier New';"> </span> </p> <p> <strong><span style="font-size:10pt;font-family:'Courier New';"> </span></strong> </p> <p> <strong><span style="font-size:10pt;font-family:'Courier New';">RESULT:</span></strong> </p> <p> <span style="font-size:10pt;font-family:'Courier New';"> </span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the sequence of single strand of DNA:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';"> </span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the sequences of multiple strands of DNA:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';"><span> </span>TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';"><span> </span>TCCTCGGGTCGATGCGATAGCTAGCTAGATCTT</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the result of chomp:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC TCCTCGGGTCGATGCGATAGCTAGCTAGATCTT</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the result of chop unction:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTG TCCTCGGGTCGATGCGATAGCTAGCTAGATCT</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the result of join:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGTCCTCGGGTCGATGCGATAGCTAGCTAGATCT</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the result of complementary:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">ATGACACCGGCACGCACCGACGGCAACGCGACAGGAGCCCAGCTACGCTATCGATCGATCTAGA</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the transcribed RNA:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">AUGACACCGGCACGCACCGACGGCAACGCGACAGGAGCCCAGCUACGCUAUCGAUCGAUCUAGA</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the length of RNA:64</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the total nucleotides:in RNA:64</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the total number of GC in DNA :7:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the GC percentage:10.9375</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the total number of Adenines:18</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the start and stop codon:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">startACACCGGCACGCACCGACGGCAACGCGACAGGAGCCCAGCUACGCUAUCGAUCGAUCStopA</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">the result of chop:</span> </p> <p> <span style="font-size:10pt;font-family:'Courier New';">startACACCGGCACGCACCGACGGCAACGCGACAGGAGCCCAGCUACGCUAUCGAUCGAUCStop</span> </p>
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