Bio SeqUtils
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Bio::SeqUtils - Additional methods for PrimarySeq objects
Package variables
No package variables defined.
Included modules
    use Bio::SeqUtils;
# get a Bio::PrimarySeqI compliant object, $seq, somehow
$util = new Bio::SeqUtils;
$polypeptide_3char = $util->seq3($seq);
# or
$polypeptide_3char = Bio::SeqUtils->seq3($seq);
# set the sequence string (stored in one char code in the object) Bio::SeqUtils->seq3($seq, $polypeptide_3char); # translate a sequence in all six frames @seqs = Bio::SeqUtils->translate_6frames($seq);
This class is a holder of methods that work on Bio::PrimarySeqI-
compliant sequence objects, e.g. Bio::PrimarySeq and
Bio::Seq. These methods are not part of the Bio::PrimarySeqI
interface and should in general not be essential to the primary function
of sequence objects. If you are thinking of adding essential
functions, it might be better to create your own sequence class.
See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more.
The methods take as their first argument a sequence object. It is
possible to use methods without first creating a SeqUtils object,
i.e. use it as an anonymous hash.
The first two methods, seq3() and seq3in(), give out or read in protein
sequences coded in three letter IUPAC amino acid codes.
The next two methods, translate_3frames() and translate_6frames(), wrap
around the standard translate method to give back an array of three
forward or all six frame translations.
Methods description
seq3code    nextTop
 Title   : seq3
Usage : $string = Bio::SeqUtils->seq3($seq)
Read only method that returns the amino acid sequence as a string of three letter codes. alphabet has to be 'protein'. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa'. A noncoded aminoacid selenocystein is recognized (Sec, U). Returns : A scalar Args : character used for stop in the protein sequence optional, defaults to '*' string used to separate the output amino acid codes, optional, defaults to ''
 Title   : seq3in
Usage : $string = Bio::SeqUtils->seq3in($seq, 'MetGlyTer')
Method for in-place changing of the sequence of a Bio::PrimarySeqI sequence object. The three letter amino acid input string is converted into one letter code. Any unknown character triplet, including the default 'Xaa', is converted into 'X'. Returns : Bio::PrimarySeq object; Args : character to be used for stop in the protein seqence, optional, defaults to '*' character to be used for unknown in the protein seqence, optional, defaults to 'X'
 Title   : translate_3frames
Usage : @prots = Bio::SeqUtils->translate_3frames($seq)
Function: Translate a nucleotide sequence in three forward frames.
The IDs of the sequences are appended with '-0F', '-1F', '-2F'.
Returns : An array of seq objects
Args : sequence object
same arguments as to Bio::PrimarySeqI::translate
 Title   : translate_6frames
Usage : @prots = Bio::SeqUtils->translate_6frames($seq)
Function: translate a nucleotide sequence in all six frames
The IDs of the sequences are appended with '-0F', '-1F', '-2F',
'-0R', '-1R', '-2R'.
Returns : An array of seq objects
Args : sequence object
same arguments as to Bio::PrimarySeqI::translate
 Title   : valid_aa
Usage : my @aa = $table->valid_aa
Function: Retrieves a list of the valid amino acid codes.
The list is ordered so that first 21 codes are for unique
amino acids. The rest are ['B', 'Z', 'X', '*'].
Returns : array of all the valid amino acid codes
Args : [optional] $code => [0 -> return list of 1 letter aa codes,
1 -> return list of 3 letter aa codes,
2 -> return associative array of both ]
Methods code
    %ONECODE =
    ('Ala' => 'A', 'Asx' => 'B', 'Cys' => 'C', 'Asp' => 'D',
     'Glu' => 'E', 'Phe' => 'F', 'Gly' => 'G', 'His' => 'H',
     'Ile' => 'I', 'Lys' => 'K', 'Leu' => 'L', 'Met' => 'M',
     'Asn' => 'N', 'Pro' => 'P', 'Gln' => 'Q', 'Arg' => 'R',
     'Ser' => 'S', 'Thr' => 'T', 'Val' => 'V', 'Trp' => 'W',
     'Xaa' => 'X', 'Tyr' => 'Y', 'Glx' => 'Z', 'Ter' => '*',
     'Sec' => 'U'

    ('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',
     'Y' => 'Tyr', 'Z' => 'Glx', 'X' => 'Xaa', '*' => 'Ter',
     'U' => 'Sec'
sub seq3 {
   my ($self, $seq, $stop, $sep ) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
       $self->throw('Not a Bio::PrimarySeqI object but [$self]');
   $seq->alphabet eq 'protein' ||
       $self->throw('Not a protein sequence');

   if (defined $stop) {
       length $stop != 1 and $self->throw('One character stop needed, not [$stop]');
       $THREECODE{$stop} = "Ter";
   $sep ||= '';

   my $aa3s;
   foreach my $aa  (split //, uc $seq->seq) {
       $THREECODE{$aa} and $aa3s .= $THREECODE{$aa}. $sep, next;
       $aa3s .= 'Xaa'. $sep;
   $sep and substr($aa3s, -(length $sep), length $sep) = '' ;
   return $aa3s;
sub seq3in {
   my ($self, $seq, $string, $stop, $unknown) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
       $self->throw('Not a Bio::PrimarySeqI object but [$self]');
   $seq->alphabet eq 'protein' ||
       $self->throw('Not a protein sequence');

   if (defined $stop) {
       length $stop != 1 and $self->throw('One character stop needed, not [$stop]');
       $ONECODE{'Ter'} = $stop;
   if (defined $unknown) {
       length $unknown != 1 and $self->throw('One character stop needed, not [$unknown]');
       $ONECODE{'Xaa'} = $unknown;

   my ($aas, $aa3);
   my $length = (length $string) - 2;
   for (my $i = 0 ; $i < $length ; $i += 3)  {
       $aa3 = substr($string, $i, 3);
       $ONECODE{$aa3} and $aas .= $ONECODE{$aa3}, next;
       $aas .= 'X';
   return $seq;
sub translate_3frames {
    my ($self, $seq, @args ) = @_;
    $self->throw('Object [$seq] '. 'of class ['. ref($seq).  ']  can not be translated.')
	unless $seq->can('translate');

    my ($stop, $unknown, $frame, $tableid, $fullCDS, $throw) = @args;
    my @seqs;
    my $f = 0;
    while ($f != 3) {
        my $translation = $seq->translate($stop, $unknown,$f,$tableid, $fullCDS, $throw );
	$translation->id($seq->id. "-". $f. "F");
	push @seqs, $translation;

    return @seqs;
sub translate_6frames {
    my ($self, $seq, @args ) = @_;
    my @seqs = $self->translate_3frames($seq, @args);
    my @seqs2 = $self->translate_3frames($seq, @args);
    foreach my $seq2 (@seqs2) {
	my ($tmp) = $seq2->id;
	$tmp =~ s/F$/R/g;
    return @seqs, @seqs2;
sub valid_aa {
   my ($self,$code) = @_;

   if( ! $code ) { 
       my @codes;
       foreach my $c ( sort values %ONECODE ) {
	   push @codes, $c unless ( $c =~ /[BZX\*]/ );
       push @codes, qw(B Z X *); # so they are in correct order ?
return @codes; } elsif( $code == 1 ) { my @codes; foreach my $c ( sort keys %ONECODE ) { push @codes, $c unless ( $c =~ /(Asx|Glx|Xaa|Ter)/ ); } push @codes, ('Asx', 'Glx', 'Xaa', 'Ter' ); return @codes; } elsif( $code == 2 ) { my %codes = %ONECODE; foreach my $c ( keys %ONECODE ) { my $aa = $ONECODE{$c}; $codes{$aa} = $c; } return %codes; } else { $self->warn("unrecognized code in ".ref($self)." method valid_aa()"); return (); } } 1;
General documentation
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AUTHOR - Heikki LehvaslaihoTop
     EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _