Bio::Tools::OAF - Ornithine decarboxylase Antizyme Finder (bioperl library)

Take a sequence object from, say, an inputstream, and find an eukaryotic ornithine decarboxylase antizyme. HMM profiles are used in order to identify location, frame and orientation of such gene.

Creating the OAF object, e.g.:

my $inputstream = Bio::SeqIO->new( -file => 'seqfile', -format => 'fasta' );
my $seqobj = $inputstream->next_seq();
my $OAF_obj = Bio::Tools::OAF->new( $seqobj );

Obtain an array holding the start point, the stop point, the DNA sequence and amino-acid sequence, eg:

my $array_ref = $OAF_obj->{'_result'} if ( $OAF_obj->find() );

Display result in genbank format, eg:

$OAF_obj->show( 'genbank' );

Bio::Tools::OAF is a featherweight object for identifying ornithine decarboxylase antizymes. The sequences should not be longer than 20kb. The returned array includes the location, the sequence and the statistic for the putative ornithine decarboxylase antizyme gene. Fully functional with mRNA and EST sequence, no intron allowed.

See Synopsis above for the object creation code.

#!/usr/bin/perl -w
use strict;

use Bio::Seq;
use Bio::Tools::OAF;

my $inseq = Bio::SeqIO->new( '-file' => "< $yourfile", -format => 'fasta' );
while (my $seq = $inseq->next_seq) {
  my $OAF_obj = Bio::Tools::OAF->new( $seq, 11 );
  if ( $OAF_obj->find() ) {
    $OAZ_obj->show( 'genbank' );
  } else {
    print "  no hit!\n";
  }
}

To use this module you need Bioperl (http://www.bioperl.org/) modules, HMMER distribution (http://hmmer.janelia.org/), Blast (http://www.ncbi.nlm.nih.gov/BLAST/download.shtml) and FASTA distribution (ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/) if using whole genome search.

Title

new

Usage

my $nb = Bio::Tools::OAF->new( $seqobj, $table, $aug, $hmm, $fs );

Function

Initialize OAF object.

Returns

An OAF object.

Args

$seqobj (mandatory) PrimarySeqI object (dna or rna),
$table (optional) translation table/genetic code number (default 1),
$aug (optional) use other start codon than AUG (default 0),
$hmm (optional) path to hmm profiles by default OAF looks at ./oaz.hmm,
$fs (optional) path to frameshift hmm profiles by default OAF looks at ./oaz.fs.hmm,

Title

find

Usage

my $bool = $OAF_obj->find( $evalue, $strand, $start, $end );

Function

Identify ornithine decarboxylase antizyme protein.

Returns

A boolean. If a release factor is found, the detailed result is then store in the table $OAF_obj->{'_result'}, the elements of the current array are:

my @CDSData = $OAF_obj->{'_result'};
print "$CDSData[0]\n";  # detailed position of the sequence [string]
print "$CDSData[1]\n";  # start position [integer]
print "$CDSData[2]\n";  # stop position [integer]
print "$CDSData[3]\n";  # strand (1 direct, -1 reverse) [integer]
print "$CDSData[4]\n";  # Protein name [string]
print "$CDSData[5]\n";  # Gene Name [string]
print "$CDSData[6]\n";  # Remarques and HMMs e-values [string]
print "$CDSData[7]\n";  # DNA sequence [string]
print "$CDSData[8]\n";  # Protein sequence [string]

The HMMs results are store in the tables $OAF_obj->{'_hmmfs'} and $OAF_obj->{'_hmmoaz'}:

my @HMMData0 = $OAF_obj->{'_hmmfs'};  # HMM details for the 5' part of the sequence
print "HMMData0[0]\n";  # HMM profile name [string]
print "HMMData0[1]\n";  # OAZ paralog id [integer]
print "HMMData0[2]\n";  # HMM score [integer]
print "HMMData0[3]\n";  # start position [integer]
print "HMMData0[4]\n";  # stop position [integer]
print "HMMData0[5]\n";  # strand (1 direct, -1 reverse) [integer]

my @HMMData1 = $OAF_obj->{'_hmmoaz'};  # HMM details for the 3' part of the sequence
print "HMMData1[0]\n";  # HMM profile name [string]
print "HMMData1[1]\n";  # OAZ paralog id [integer]
print "HMMData1[2]\n";  # HMM score [integer]
print "HMMData1[3]\n";  # start position [integer]
print "HMMData1[4]\n";  # stop position [integer]
print "HMMData1[5]\n";  # strand (1 direct, -1 reverse) [integer]

The sequences issues are separately store:

print '5\' of the CDS is missing: ', $OAF_obj->{'_no5'} ? 'yes' : 'no', "\n";
print '3\' of the CDS is missing: ', $OAF_obj->{'_no3'} ? 'yes' : 'no' . "\n";
print 'The position of the initiation codon is identified: ', $OAF_obj->{'_noaug'} ? 'no' : 'yes', "\n";

Args

$evalue (optional) set the E-value (expected) threshold. Default is 1e-40,
$strand (optional) strand where search should be done (1 direct, -1 reverse or 0 both). Default is 0,
$start (optional) coordinate of the first nucleotide. Useful for coordinate calculation when first is not 1. Default is 1,
$end (optional) coordinate of the last nucleotide. Default is the sequence length.

Title

show

Usage

$OAF_obj->show( $outstyle );

Function

Print result in various style.

Returns

none.

Args

$outstyle (mandatory) 'fasta', 'genbank', 'raw' or 'xml' style. Note: the XML style requires the call of the function with 'xml-begin' to initialise the output, and 'xml-end' to close the output.

Title

getHits

Usage

my @hits = Bio::Tools::OAF->getHits( $evalue, $seq, $ref );

Function

Quick localization of OAZs (use FASTA).

Returns

Array of hits start/stop positions:

print join( "\n", @hits );

Args

$evalue (mandatory) set the E-value threshold,
$seq (mandatory) PrimarySeqI object (dna or rna),
$ref (optional) path to fasta reference file, by default OAF look at ./OAZ.fasta,

Title

ortholog

Usage

my $bool = Bio::Tools::OAF->ortholog( $file, $evalue, $format, $aug, $remote, $hmm, $fs, $bank, $filter, $verbose );

Function

Full BLAST search...

Returns

A boolean.

Args

$file (mandatory) name of the file of protein sequence(s) (FASTA file format),
$evalue (optional) set the E-value threshold,
$format (optional) output format: 'fasta', 'genbank', 'raw' or 'xml' style,
$aug (optional) use other start codon than AUG (default 0),
$remote (optional) Configure the program to use the remote BLAST server of the NCBI (1) rather than with a local BLAST (0). By default the local Blast is used (0),
$hmm (optional) path to hmm profiles by default OAF looks at ./oaz.hmm,
$fs (optional) path to frameshift hmm profiles by default OAF looks at ./oaz.fs.hmm,
$bank (optional) set the database used by the ortho[log] mode. If the remote NCBI option in set, this set the database used for the initial blast search. Available databases include 'refseq_rna' (Complete genomes and chromosomes from the NCBI Reference Sequence project), 'est' (Sequences from EST divisions). By default 'est' is used,
$filter (optional) set the filter. Normally OAF.pl show all sequences identified whether the sequence may be the putative/ambiguous, because of a truncated EST, a sequence error or a missing -1 frameshift. By default there is no filter (0), you can filter for the non-ambiguous hits only (1) or the ambiguous hits only (2),
$verbose (optional) print more possibly useful stuff, such as the individual scores for each sequence.

This software and documentation are licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.