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# Only we need to change the if where the pattern was found
# Now check the sequence, collected in its entirety,

# for the given pattern

# and check its position in the sequence

  if ($secuencia_total =~ /$patron/) {

   $posicion=length($`)+1;

   print "The sequence query_seq.txt contains the pattern $patron in the following position $posicion\n";
  } else {

  print "The sequence query_seq.txt doesn't contains the pattern $patron\n";

  }

���㰱�����Ƶ�ȣ�Calculus of aminoacid frequences��:

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#!/usr/bin/perl
# Calculates the frequency of aminoacid in a proteinic sequence
# Gets the file name from the command line
# (SWISS-PROT formatted)
# Also can be asked with print from the <STDIN>
if (!$ARGV[0]) {print "The execution line shall be: program.pl file_swissprot\n";}
$fichero = $ARGV[0];
# Initialize the variable $errores
my $errores=0;
# Open the file for reading
open (FICHA, "$fichero") || die "problem opening the file $fichero\n";
# First we check the sequence as did in the example 2
while (<FICHA>) {
chomp $_;
if ($_ =~ /^SQ/) {
$signal_good = 1;
} elsif ($signal_good == 1) {
   last if ($_ =~ /^\/\//);
   $_ =~ s/\s//g;
   $secuencia.=$_;
}
}
close (FICHA);
# Now use a curl that checks every position of the aminoacid
# in the sequence (from a funcion of its own,that can be used after in other
# programs)
comprueba_aa ($secuencia);
# Print the results to the screen
# First the  20 aminoacids and then the array with their frequencies
# In this case 'sort' can't be used in foreach, 
# because the array contains the frequencies (numbers)
print"A\tC\tD\tE\tF\tG\tH\tI\tK\tL\tM\tN\tP\tQ\tR\tS\tT\tV\tW\tY\n";
foreach $each_aa (@aa) {
print "$each_aa\t";
}
# Ten it gives the possible errors
# and ends the program
print "\nerrores = $errores\n";
exit;
# Functions
# This one calculates each aminoacid frequency
# from a proteinic sequence
sub comprueba_aa {
# Gets the sequence
my ($secuencia)=@_;
# and runs aminoacid by aminoacid, using a for running
# from 0 until the sequence length
for ($posicion=0 ; $posicion<length $secuencia ; $posicion++ ) {
# Gets the aminoacid
$aa = substr($secuencia, $posicion, 1);
# and checks which one is using if
# when it is checked it aggregates 1 to the correspondant frequency
# in an array using a pointer for each one
# ordered in alphabetic way
if ( $aa eq 'A' ) {
$aa[0]++;
} elsif ( $aa eq 'C' ) {
$aa[1]++;
} elsif ( $aa eq 'D' ) {
$aa[2]++;
} elsif ( $aa eq 'E' ) {
$aa[3]++;
} elsif ( $aa eq 'F' ) {
$aa[4]++;
} elsif ( $aa eq 'G' ) {
$aa[5]++;
} elsif ( $aa eq 'H' ) {
$aa[6]++;
} elsif ( $aa eq 'I' ) {
$aa[7]++;
} elsif ( $aa eq 'K' ) {
$aa[8]++;
} elsif ( $aa eq 'L' ) {
$aa[9]++;
} elsif ( $aa eq 'M' ) {
$aa[10]++;
} elsif ( $aa eq 'N' ) {
$aa[11]++;
} elsif ( $aa eq 'P' ) {
$aa[12]++;
} elsif ( $aa eq 'Q' ) {
$aa[13]++;
} elsif ( $aa eq 'R' ) {
$aa[14]++;
} elsif ( $aa eq 'S' ) {
$aa[15]++;
} elsif ( $aa eq 'T' ) {
$aa[16]++;
} elsif ( $aa eq 'V' ) {
$aa[17]++;
} elsif ( $aa eq 'W' ) {
$aa[18]++;
} elsif ( $aa eq 'Y' ) {
$aa[19]++;
# If the aminoacid is not found
# it aggregates 1 to the errors
} else {
print "ERROR: Aminoacid not found: $aa\n";
$errores++;
}
}
# Finally returns to the frequency array
return @aa;
}

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#!/usr/bin/perl
# Translates an ADN sequence from an EMBL fiche
# to the aminoacid correspondant
# Gets the file name from the command line
# (SWISS-PROT formatted)
# Also can be asked with print from the <STDIN>
if (!$ARGV[0]) {print "The program line shall be: program.pl ficha_embl\n";}
$fichero = $ARGV[0];
# Open the file for reading
open (FICHA, "$fichero") || die "problem opening the file $fichero\n";
# First we check the sequence as did in the example 2
while (<FICHA>) {
chomp $_;
if ($_ =~ /^FT CDS/) {
$_ =~ tr/../ /;
($a1,$a2,$a3,$a4) = split (" ",$_);
}
elsif ($_ =~ /^SQ/) {
$signal_good = 1;
} elsif ($signal_good == 1) {
last if ($_ =~ /^\/\//);
# Eliminate numbers and spaces
$_ =~ tr/0-9/ /;
$_ =~ s/\s//g;
$secuencia.=$_;
}
}
close (FICHA);
# Now we define an associate array with the correpondence
# of every aminoacids with their nucleotide
# correspondants (also in an own function,
# for if the same genetic code is used in other program
my(%codigo_genetico) = (
'TCA' => 'S',# Serine
'TCC' => 'S',# Serine
'TCG' => 'S',# Serine
'TCT' => 'S',# Serine
'TTC' => 'F',# Fenilalanine
'TTT' => 'F',# Fenilalanine
'TTA' => 'L',# Leucine
'TTG' => 'L',# Leucine
'TAC' => 'Y',# Tirosine
'TAT' => 'Y',# Tirosine
'TAA' => '*',# Stop
'TAG' => '*',# Stop
'TGC' => 'C',# Cysteine
'TGT' => 'C',# Cysteine
'TGA' => '*',# Stop
'TGG' => 'W',# Tryptofane
'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',# Hystidine
'CAT' => 'H',# Hystidine
'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',# Methionina
'ACA' => 'T',# Treonina
'ACC' => 'T',# Treonina
'ACG' => 'T',# Treonina
'ACT' => 'T',# Treonina
'AAC' => 'N',# Asparagina
'AAT' => 'N',# Asparagina
'AAA' => 'K',# Lisina
'AAG' => 'K',# Lisina
'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',# Glicine
'GGC' => 'G',# Glicine
'GGG' => 'G',# Glicine
'GGT' => 'G',# Glicine
);
# Translate every codon in its correspondant aminoacid
# and aggregates to the proteinic sequence
print $a3;
for($i=$a3 - 1; $i < $a4 - 3 ; $i += 3) {
$codon = substr($secuencia,$i,3);
# Pass the codon from subcase (EMBL format) to uppercase
$codon =~ tr/a-z/A-Z/;
$protein.= codon2aa($codon);
}
print "This proteinic sequence of the gen:\n$secuencia\nis the following:\n$protein\n\n";
exit;

Bibliographic References

• http://bioperl.org/
  
  
• http://changjiang.whlib.ac.cn/pylorus/download/book/Beginning%20Perl%20for%20Bioinformatics/contents.html
  
  

• http://www.unix.org.ua/orelly/perl/prog3/
  
  

• Example files :
  - human_kinases_swissprot.txt
  - query_seq.txt
  - ecoli_embl.txt