G::Seq
AminoAcid
G::Seq::AminoAcid - Perl extension for blah blah blah
|
| Globals (from use vars definitions) |
| @EXPORT |
| $VERSION |
| @EXPORT_OK |
| Privates (from my definitions) |
| %pK = ( C=>8.5, D=>3.9, E=>4.1, H=>6.5, K=>10.8, R=>12.5, Y=>10.1, N_term=>8.6, C_term=>3.6 ) |
| %mass = ( A=>82.09, C=>121.16, D=>133.10, E=>147.13, F=>165.19, G=>75.07, H=>155.16, I=>131.17, K=>146.19, L=>131.17, M=>149.21, N=>132.12, P=>115.13, Q=>146.15, R=>174.20, S=>105.09, T=>119.12, V=>117.15, W=>204.22, Y=>181.19 ) |
| %residue = ( A=>71.0786, B=>114.5960, C=>103.1386, D=>115.0884, E=>129.1152, F=>147.1762, G=>57.0518, H=>137.1408, I=>113.1590, K=>128.1736, L=>113.1590, M=>131.1926, N=>114.1036, P=>97.1164, Q=>128.1304, R=>156.1870, S=>87.0780, T=>101.1048, V=>99.1322, W=>186.2128, X=>144.0000, Y=>163.1756, Z=>128.6228 ) |
| %monoisotopic = ( A=>71.04, C=>103.01, D=>115.03, E=>129.04, F=>147.07, G=>57.02, H=>137.06, I=>113.08, K=>128.09, L=>113.08, M=>131.04, N=>114.04, P=>97.05, Q=>128.06, R=>156.10, S=>87.03, T=>101.05, V=>99.07, W=>186.08, Y=>163.06 ) |
| %dayhoff = ( A=>8.6, B=>0.0, C=>2.9, D=>5.5, E=>6.0, F=>3.6, G=>8.4, H=>2.0, I=>4.5, K=>6.6, L=>7.4, M=>1.7, N=>4.3, P=>5.2, Q=>3.9, R=>4.9, S=>7.0, T=>6.1, V=>6.6, W=>1.3, X=>0.0, Y=>3.4, Z=>0.0) |
| %charge = ( A=>0, B=>-0.5, C=>0, D=>-1, E=>-1, F=>0, G=>0, H=>0.5, I=>0, K=>1, L=>0, M=>0, N=>0, P=>0, Q=>0, R=>1, S=>0, T=>0, V=>0, W=>0, X=>0, Y=>0, Z=>-0.5 ) |
| %three2one = reverse %one2three |
| %one2three = ( A=>"Ala", B=>"Asx", C=>"Cys", D=>"Asp", E=>"Glu", F=>"Phe", G=>"Gly", H=>"His", I=>"Ile", K=>"Lys", L=>"Leu", M=>"Met", N=>"Asn", P=>"Pro", Q=>"Gln", R=>"Arg", S=>"Ser", T=>"Thr", V=>"Val", W=>"Trp", X=>"Xxx", Y=>"Tyr", Z=>"Glx" ) |
Stub documentation for G::Seq::AminoAcid was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
Blah blah blah.
|
Methods description
Author: Misa Nakanishi (dora@g-language.org)
Usage: amino_info(string $aminoseq)
Options: None.
Description: Prints basic amino acid sequence information
History: created 2001.04.04
Tuned by Kazuharu Arakawa (gaou@g-language.org)
Author: Kazuharu Arakawa (gaou@g-language.org)
Usage: double $pI = calc_pI(string $aminoseq);
Options: None.
Description: Calculates isoelectric point of given amino acid sequence.
History: created 2001.04.04
Author: Kazuharu Arakawa (gaou@g-language.org)
Usage: double $mass = peptide_mass(string $aminoseq);
Options: None.
Description: Calculates mass of given amino acid sequence.
History: created 2001.04.04
Methods code
sub DESTROY
{ my $self = shift;
}
sub _charge
{ my $first = shift;
my $second = shift;
my $cr = 10 ** ($first - $second);
return $cr / (1 + $cr);
}
sub amino_info
{ my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $output = opt_val("output");
my %amino;
my ($mw, $chrg, $iso);
foreach my $char (split(//, $gb->{SEQ})){
$amino{$char}++;
$mw += $mass{$char};
$chrg += $charge{$char};
}
msg_send("Amino Info\n\n");
msg_send(sprintf("AminoInfo of %s from 1 to %d\n\n",
$gb->{LOCUS}->{id}, length($gb->{SEQ})));
msg_send(sprintf("Molecular weight = %.2f Residues = %d\n",
"$mw", length($gb->{SEQ})));
msg_send(sprintf("Average Weight = %.2f Charge = %s\n",
$mw/length($gb->{SEQ}), "$chrg"));
msg_send(sprintf("Isoelectric Point = %.4f\n",
calc_pI($gb->{SEQ})));
msg_send(sprintf("%-15.15s %-15.15s %-15.15s %15.15s\n",
"Residue", "Number", "Mole\%", "DayhoffStat"));
foreach my $char (sort keys %amino){
msg_send(sprintf("%-15.15s %-15.15s %-15.15s %15.15s\n",
sprintf("%s = %s", $char, $one2three{$char}),
$amino{$char},
sprintf("%.3f", $amino{$char} / length($gb->{SEQ}) * 100),
sprintf("%.3f", $dayhoff{$char} ? ($amino{$char} / length($gb->{SEQ}) / $dayhoff{$char} * 100) : 0)
));
}
msg_send("\nProperty Residues Number Mole\%\n");
msg_send(sprintf("Tiny (A+C+G+S+T) %-15.15s %.3f\n",
$amino{A}+$amino{C}+$amino{G}+$amino{S}+$amino{T},
($amino{A}+$amino{C}+$amino{G}+$amino{S}+$amino{T})/length($gb->{SEQ})*100
));
msg_send(sprintf("Small (A+B+C+D+G+N+P+S+T+V) %-15.15s %.3f\n",
$amino{A}+$amino{B}+$amino{C}+$amino{D}+$amino{G}+$amino{N}+$amino{P}+$amino{S}+$amino{T}+$amino{V},
($amino{A}+$amino{B}+$amino{C}+$amino{D}+$amino{G}+$amino{N}+$amino{P}+$amino{S}+$amino{T}+$amino{V})/length($gb->{SEQ})*100
));
msg_send(sprintf("Aliphatic (I+L+V) %-15.15s %.3f\n",
$amino{I}+$amino{L}+$amino{V},
($amino{I}+$amino{L}+$amino{V})/length($gb->{SEQ})*100
));
msg_send(sprintf("Aromatic (F+H+W+Y) %-15.15s %.3f\n",
$amino{F}+$amino{H}+$amino{W}+$amino{Y},
($amino{F}+$amino{H}+$amino{W}+$amino{Y})/length($gb->{SEQ})*100
));
msg_send(sprintf("Non-polar (A+C+F+G+I+L+M+P+V+W+Y) %-15.15s %.3f\n",
$amino{A}+$amino{C}+$amino{F}+$amino{G}+$amino{I}+$amino{L}+$amino{M}+$amino{P}+$amino{V}+$amino{W}+$amino{Y},
($amino{A}+$amino{C}+$amino{F}+$amino{G}+$amino{I}+$amino{L}+$amino{M}+$amino{P}+$amino{V}+$amino{W}+$amino{Y})/length($gb->{SEQ})*100
));
msg_send(sprintf("Polar (D+E+H+K+N+Q+R+S+T+Z) %-15.15s %.3f\n",
$amino{D}+$amino{E}+$amino{H}+$amino{K}+$amino{N}+$amino{Q}+$amino{R}+$amino{S}+$amino{T}+$amino{Z},
($amino{D}+$amino{E}+$amino{H}+$amino{K}+$amino{N}+$amino{Q}+$amino{R}+$amino{S}+$amino{T}+$amino{Z})/length($gb->{SEQ})*100
));
msg_send(sprintf("Charged (B+D+E+H+K+R+Z) %-15.15s %.3f\n",
$amino{B}+$amino{D}+$amino{E}+$amino{H}+$amino{K}+$amino{R}+$amino{Z},
($amino{B}+$amino{D}+$amino{E}+$amino{H}+$amino{K}+$amino{R}+$amino{Z})/length($gb->{SEQ})*100
));
msg_send(sprintf("Basic (H+K+R) %-15.15s %.3f\n",
$amino{H}+$amino{K}+$amino{R},
($amino{H}+$amino{K}+$amino{R})/length($gb->{SEQ})*100
));
msg_send(sprintf("Acidic (B+D+E+Z) %-15.15s %.3f\n",
$amino{B}+$amino{D}+$amino{E}+$amino{Z},
($amino{B}+$amino{D}+$amino{E}+$amino{Z})/length($gb->{SEQ})*100
));
}
sub calc_pI
{ my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $pI = 7.0;
my $tmpcharge = 0;
my $step = 3.5;
my %num;
$num{C} = $gb->{SEQ} =~ tr/C/C/;
$num{D} = $gb->{SEQ} =~ tr/D/D/;
$num{E} = $gb->{SEQ} =~ tr/E/E/;
$num{H} = $gb->{SEQ} =~ tr/H/H/;
$num{K} = $gb->{SEQ} =~ tr/K/K/;
$num{R} = $gb->{SEQ} =~ tr/R/R/;
$num{Y} = $gb->{SEQ} =~ tr/Y/Y/;
while(1){
my $charge =
- _charge($pI, $pK{C_term})
- $num{C} * _charge($pI, $pK{C})
- $num{D} * _charge($pI, $pK{D})
- $num{E} * _charge($pI, $pK{E})
- $num{Y} * _charge($pI, $pK{Y})
+ $num{H} * _charge($pK{H}, $pI)
+ $num{K} * _charge($pK{K}, $pI)
+ $num{R} * _charge($pK{R}, $pI)
+ _charge($pK{N_term}, $pI);
last if(sprintf("%.5f", $charge) == sprintf("%.5f", $tmpcharge));
if($charge > 0){
$pI += $step;
}else{
$pI -= $step;
}
$tmpcharge = $charge;
$step /= 2;
}
return $pI;}
sub mass
{ my $this = shift;
return %mass;}
sub new
{ my $pkg = shift;
my $this = {};
bless $this;
return $this;}
sub one2three
{ my $this = shift;
return %one2three;}
sub peptide_mass
{ my @argv = opt_get(@_);
my $gb = opt_as_gb(shift @argv);
my $totmass = 0;
foreach my $amino (split(//, $gb->{SEQ})){
$totmass += $mass{$amino};
}
return $totmass;}
sub three2one
{ my $this = shift;
return %three2one;}
General documentation