Outline Lecture 13
April 12, 2006

I. Discuss Homology Modeling
A. Fixing Alignment Clashes
B. Evaluation of the Model
II. Introduction to Perl
A. Running Perl
B. Scalar variables
C. Binding operator =~
D. String substitution and translation
E. Reading Files

#Program 1########################################################
#!/usr/bin/perl
# my first Perl program
print "Hello world \n";

#Program 2########################################################
#!/usr/bin/perl
print "4+5\n";
print 4+5 , "\n";
print "4+5=" , 4+5 , "\n";
#Program 3########################################################
#!/usr/bin/perl
#put some values in variables
$sequences_analyzed = 200  ;
$new_sequences = 21   ;
#now we will do the work
$percent_new_sequences =( $new_sequences / 
$sequences_analyzed) *100  ;
print "% of new sequences = " , $percent_new_sequences,"\n";

#Program 4########################################################
#!/usr/bin/perl –w
use strict;
# Store the DNA sequence in a variable
$DNA1 = 'ACGGGAGGACGGGAA';
$DNA2 = 'ATTACTACGGCATTAGC';
# print the DNA sequence out with a line feed
print $DNA1,"\n";
print $DNA2,"\n";
#concatenate the strings Note error
$DNA3 = $DNA1 . DNA2
print "The concatenated string are";
print "$DNA3\n";
# alternately
$DNA3 = "$DNA1 $DNA2 \n";
print $DNA3;
# finish the program
exit;

#Program 5########################################################
# Store the DNA sequence in a variable
$DNA = 'ACGGGAGGACGGGAAATTACTACGGCATTAGC';
# print the DNA sequence out with a line feed
print "Here is the DNA \n";
print $DNA,"\n";
# convert the DNA into RNA
$RNA = $DNA;
$RNA =~ s/T/U/g;
# print the results
print "Here is the transcribed RNA: \n";
print "$RNA\n";
# exit the program
exit;

#Program 6########################################################
# Store the DNA sequence in a variable
$DNA = 'ACGGGAGGACGGGAAATTACTACGGCATTAGC';
# print the DNA sequence out with a line feed
print $DNA,"\n";
# reverse the DNA string 3'-5'
$revcom = $DNA;
$revcom =~ tr/ACGTacgt/TGCAtgca/;
# print the results
print "Here is the complement 3'-5': \n\n";
print "$revcom\n";
#  reverse the strand
$revcom = reverse $revcom;
print "Here is the complement 5'-3': \n\n";
print "$revcom\n";
# exit the program
exit;

#Program 7########################################################
print "Enter your name: ";
$name = <>;
print "Hello $name, happy to meet you!\n";
chomp $name;
print "Hello $name, happy to meet you!\n"; 

#Program 8########################################################

Sample Data file  save to fragment.txt
MNIDDKLEGLFLKCGGIDEMQSSRTMVVMGGVSGQSTVSGELQD
SVLQDRSMPHQEILAADEVLQESEMRQQDMISHDELMVHEETVKNDEEQMETHERLPQ
GLQYALNVPISVKQEITFTDVSEQLMRDKKQIR

#Program 8########################################################
# name the file to read
$protname= 'fragment.txt';
# open the file and associate a file handle
open(PROTFILE,$protname);
# now read a line and print it
$protein = <PROTFILE>;
# close the file because we are done
close PROTFILE;
# print the the results
print "Here is the protein \n\n";
print $protein,"\n";
exit;

#Program 9########################################################
# name the file to read
$protname= 'fragment.txt';
# open the file and associate a file handle
open(protfile,$protname);
# now read the file into an array
@protein = <protfile>;
# close the file because we are done
close protfile;
# print the the results
print "Here is the protein \n\n";
print @protein
# print the second record
print "/n The second record is \n";
print $protein[2],"\n";
exit;

#Program 10########################################################
# read the file name
print "Please type the name of the file to read: "
$protname= <STDIN>;
#chomp $protname;
# open the file and associate a file handle
open(protfile,$protname) || die " Can not open file $protfile \n";
# now read the file in a loop
print "Reading file \"$protname\" with a while loop \n"
$count = 0;
while(<protfile>) {
        print $count, $_;
	$count = $count +1
        $protein[$count]=$_;	
	}
# close the file because we are done
close protfile;
exit;