G::Seq
AminoAcid
Summary
G::Seq::AminoAcid - Analysis methods related to amino acids.
Package variables
No package variables defined.
Included modules
Inherit
Exporter
Synopsis
No synopsis!
Description
This class is a part of G-language Genome Analysis Environment,
collecting sequence analysis methods related to amio acids.
Methods
Methods description
Name: amino_info - prints out basic amino acid sequence statistics
Description:
This method prints out basic compositional statistics of the
given amino acid sequence in a human readable manner.
Displayed information includes the following:
Molecular weight, number of residues, average residue weight, charge,
isoelectric point, number/mole/DayhoffStat of each amino acid, and
percentage of Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V),
Aliphatic (I+L+V), Aromatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),
Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R),
Acidic (B+D+E+Z) residues.
Usage:
null = amino_info($sequence);
Options:
none
Author:
Misa Nakanishi (dora@g-language.org)
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20010404-01 initial posting |
Name: calc_pI - calculates the isoelectric point of given amino acid sequence
Description:
This method calculates the isoelectric point of given amino acid sequence.
Usage:
$pI = calc_pI($aminoseq);
Options:
none
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20010404-01 initial posting |
Name: one2three - converts one letter amino acid code to three letter code
Description:
This method converts one letter amino acid code to three letter code.
Usage:
$amino = one2three($aminocid);
eg. one2three('A'); # returns 'Ala';
Options:
none
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20101105-01 added support for amino acid sequence
20010404-01 initial posting |
Name: three2one - converts three letter amino acid code to one letter code
Description:
This method converts three letter amino acid code to one letter code.
Usage:
$amino = three2one($aminocid);
eg. three2one('Ala'); # returns 'A';
Options:
none
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20101105-01 added support for amino acid sequence
20010404-01 initial posting |
Methods code
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);
my %charge = charge();
my %mass = mass();
my %dayhoff = dayhoff();
my %one2three = one2three();
foreach my $char (split(//, $gb->{SEQ})){
$amino{uc($char)}++;
$mw += $mass{uc($char)};
$chrg += $charge{uc($char)};
}
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;
my %pK = pK();
$num{C} = uc($gb->{SEQ}) =~ tr/C/C/;
$num{D} = uc($gb->{SEQ}) =~ tr/D/D/;
$num{E} = uc($gb->{SEQ}) =~ tr/E/E/;
$num{H} = uc($gb->{SEQ}) =~ tr/H/H/;
$num{K} = uc($gb->{SEQ}) =~ tr/K/K/;
$num{R} = uc($gb->{SEQ}) =~ tr/R/R/;
$num{Y} = uc($gb->{SEQ}) =~ tr/Y/Y/;
local *_charge = sub {
my $first = shift;
my $second = shift;
my $cr = 10 ** ($first - $second);
return $cr / (1 + $cr);
};
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 charge
{ my $key = shift;
my %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
);
return $charge{$key} if (length $key);
return %charge;} | sub dayhoff
{ my $key = shift;
my %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
);
return $dayhoff{$key} if (length $key);
return %dayhoff;} | sub hydropathy
{ my $key = shift;
my %hydropathy = (
A=> 1.8, C=> 2.5, D=>-3.5, E=>-3.5, F=> 2.8,
G=>-0.4, H=>-3.2, I=> 4.5, K=>-3.9, L=> 3.8,
M=> 1.9, N=>-3.5, P=>-1.6, Q=>-3.5, R=>-4.5,
S=>-0.8, T=>-0.7, V=> 4.2, W=>-0.9, Y=>-1.3
);
return $hydropathy{$key} if (length $key);
return %hydropathy;} | sub mass
{ my $key = shift;
my %mass = (
A=>89.09, 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,
X=>146, Z=>146
);
return $mass{$key} if (length $key);
return %mass;} | sub one2three
{ my $key = shift;
my $ret = '';
my %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=>"Xaa", Y=>"Tyr", Z=>"Glx",
U=>"Sec", '/'=>"TER"
);
for my $char (split(//, uc($key))){
$ret .= $one2three{$char};
}
return $ret if (length $key);
return %one2three;} | sub pK
{ my $key = shift;
my %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
);
return $pK{$key} if (length $key);
return %pK;} | sub residue
{ my $key = shift;
my %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
);
return $residue{$key} if (length $key);
return %residue;} | sub three2one
{ my $key = shift;
my $ret = '';
my %three2one = reverse one2three();
for(my $i = 0; $i < length($key); $i ++){
$ret .= $three2one{substr($key, $i, 3)};
}
return $ret if (length $key);
return reverse one2three();} | General documentation
| G::Seq::AminoAcid::charge | Top |
Name: G::Seq::AminoAcid::charge - returns the charge of a given amino acid
Description:
This method returns the charge of a given amino acid.
Usage:
$charge = G::Seq::AminoAcid::charge($aminocid);
eg. G::Seq::AminoAcid::charge('A'); # returns 0
Options:
none
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20010404-01 initial posting| G::Seq::AminoAcid::residue | Top |
Name: G::Seq::AminoAcid::residue - retunrs the mass of a given amino acid residue
Description:
This method returns the mass of a given amino acid residue.
Usage:
$mass = G::Seq::AminoAcid::residue($aminocid);
eg. G::Seq::AminoAcid::residue('A'); # returns 71.0786
Options:
none
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20010404-01 initial posting| G::Seq::AminoAcid::mass | Top |
Name: G::Seq::AminoAcid::mass - retunrs the mass of a given amino acid
Description:
This method returns the mass of a given amino acid.
Usage:
$mass = G::Seq::AminoAcid::mass($aminocid);
eg. G::Seq::AminoAcid::mass('A'); # returns 89.09
Options:
none
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20010404-01 initial posting| G::Seq::AminoAcid::hydropathy | Top |
Name: G::Seq::AminoAcid::hydropathy - returns the hydropathy of given amino acid
Description:
This method returns the hydropathy of a given amino acid.
Usage:
$hydropathy = G::Seq::AminoAcid::hydropathy($aminocid);
eg. G::Seq::AminoAcid::hydropathy('A'); # returns 1.8;
Options:
none
Author:
Haruo Suzuki (hs568@cornell.edu)
References:
1. Kyte J, Doolittle RF (1982) "A simple method for displaying the
hydropathic character of a protein", J Mol Biol, 157(1):105-32.
History:
20091204-01 initial posting