Damian at 16:49, 18 December 2009

2009-12-18T16:49:17Z

← Older revision		Revision as of 16:49, 18 December 2009
Line 1:		Line 1:
	Return to [[Week 2]]		Return to [[Week 2]]
	<br>		<br>
	Exercise 5.4 in <i>Beginning Perl for Bioinformatics</i~~></b~~>		Exercise 5.4 in <i>Beginning Perl for Bioinformatics</i>

	<pre>		<pre>

Damian at 16:48, 18 December 2009

2009-12-18T16:48:58Z

← Older revision		Revision as of 16:48, 18 December 2009
Line 1:		Line 1:

	~~#!/usr/bin/perl -w~~

	~~use strict;~~

	~~#Damian Almiron~~
	Return to [[Week 2]]		Return to [[Week 2]]
	<br>		<br>
	Exercise 5.3 in <i>Beginning Perl for Bioinformatics</i></b>		Exercise 5.4 in <i>Beginning Perl for Bioinformatics</i></b>

	<pre>		<pre>

Damian: New page: #!/usr/bin/perl -w use strict; #Damian Almiron Return to Week 2
Exercise 5.3 in Beginning Perl for Bioinformatics

 #Ex 5-4   #Pseudocode:  #Write program to c...

2009-12-18T16:36:58Z

New page: #!/usr/bin/perl -w use strict; #Damian Almiron Return to Week 2 Exercise 5.3 in Beginning Perl for Bioinformatics <pre> #Ex 5-4 #Pseudocode: #Write program to c...

New page

#!/usr/bin/perl -w

use strict;

#Damian Almiron
Return to [[Week 2]]
 
Exercise 5.3 in Beginning Perl for Bioinformatics

<pre>
#Ex 5-4

#Pseudocode:

#Write program to calculate the reverse complement of a string of DNA.

#First, get DNA sequence from user input.

#Second, calculate reverse complement using substr

#Print result

#my variables

my $DNA = 0;

my $reversecomplement = 0;

my $base = 0;

my $position = 0;

#Ask the user for a string of DNA (change it to upper)

print "Please input a string of DNA to get its reverse complement:\n\n";

$DNA = <STDIN>;

chomp $DNA;

#Calculate reverse complement (refer to pg. 80 and what if it is not uppercase)

for ($position = 0 ; $position < length $DNA ; ++$position){

$base = substr($dna, $position, 1);

if ( $base eq 'T' ) {

$reversecomplement = $reverse_dna.'A';

} elsif ( $base eq 'A' ) {

$reversecomplement = $reverse_dna.'T';

} elsif ( $base eq 'G' ) {

$reversecomplement = $reverse_dna.'C';

} elsif ( $base eq 'C' ) {

$reverse_dna = $reverse_dna.'G';

}

}

#Strip $reverse_dna of it's first character (why??????)

$reverse_dna =~ s/^0*//;

#Print result

print "The corresponding reverse complement sequence is: $reverse_dna.\n\n";

#The End

exit;
</pre>

Exercise 5.4D - Revision history

Damian at 16:49, 18 December 2009

Damian at 16:48, 18 December 2009

Damian: New page: #!/usr/bin/perl -w use strict; #Damian Almiron Return to Week 2
Exercise 5.3 in Beginning Perl for Bioinformatics
#Ex 5-4 #Pseudocode: #Write program to c...

Exercise 5.4D - Revision history

Damian at 16:49, 18 December 2009

Damian at 16:48, 18 December 2009

Damian: New page: #!/usr/bin/perl -w use strict; #Damian Almiron Return to Week 2 Exercise 5.3 in Beginning Perl for Bioinformatics #Ex 5-4 #Pseudocode: #Write program to c...

Damian: New page: #!/usr/bin/perl -w use strict; #Damian Almiron Return to Week 2
Exercise 5.3 in Beginning Perl for Bioinformatics
#Ex 5-4 #Pseudocode: #Write program to c...