Bio::Search::Tiling::TilingI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module

SYNOPSIS

Not used directly. Useful POD here for developers, however.

The interface is desgined to make the following code conversion as simple as possible:

From:

  # Bio::Search::SearchUtils-based
  while ( local $_ = $result->next_hit ) {
     printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
       $hit->significance, $hit->frac_aligned_query, $hit->num_identical);
  }
 
 

To:

  # TilingI-based
  while ( local $_ = $result->next_hit ) {
     my $tiling = Bio::Search::Tiling::MyTiling($_);
     printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
       $hit->significance, $tiling->frac_aligned_query, $tiling->num_identical);
  }
 
 

DESCRIPTION

This module provides strong suggestions for any intended HSP tiling object implementation. An object subclassing TilingI should override the methods defined here according to their descriptions below.

See the section STATISTICS METHODS for hints on implementing methods that are valid across different algorithms and report types.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Mark A. Jensen

Email maj@fortinbras.us

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

STATISTICS METHODS

The tiling statistics can be thought of as global counterparts to similar statistics defined for the individual HSPs. We therefore prescribe definitions for many of the synonymous methods defined in Bio::Search::HSP::HSPI.

The tiling statistics must be able to keep track of the coordinate systems in which both the query and subject sequences exist; i.e., either nucleotide or amino acid. This information is typically inferred from the name of the algorithm used to perform the original search (contained in "$hit_object->algorithm"). Here is a table of algorithm information that may be useful (if you trust us).

  algorithm   query on hit   coordinates(q/h)
  ---------   ------------   ---------------
   blastn      dna on dna         dna/dna
   blastp      aa  on aa           aa/aa
   blastx      xna on aa          dna/aa
  tblastn      aa  on xna          aa/dna
  tblastx      xna on xna         dna/dna
    fasta      dna on dna         dna/dna
    fasta      aa  on aa           aa/aa
    fastx      xna on aa          dna/aa
    fasty      xna on aa          dna/aa
   tfasta      aa  on xna          aa/dna
   tfasty      aa  on xna          aa/dna
  megablast    dna on dna         dna/dna
 
   xna: translated nucleotide data
 
 

Statistics methods must also be aware of differences in reporting among the algorithms. Hit attributes are not necessarily normalized over all algorithms. Devs, please feel free to add examples to the list below.

NCBI BLAST vs WU-BLAST (AB-BLAST) lengths
The total length of the alignment is reported differently between these two flavors. "$hit_object->length()" will contain the number in the denominator of the stats line; i.e., 120 in
  Identical = 34/120 Positives = 67/120
 
 

NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a. ``with gaps''). WU-BLAST uses the length of the query sequence actually aligned by the algorithm (a.k.a. ``without gaps'').

Finally, developers should remember that sequence data may or may not be associated with the HSPs contained in the hit object. This will typically depend on whether a full report (e.g, "blastall -m0") or a summary (e.g., "blastall -m8") was parsed. Statistics methods that depend directly on the sequence data will need to check that that data is present.

identities

  Title   : identities
  Alias   : num_identical
  Usage   : $num_identities = $tiling->identities()
  Function: Return the estimated or exact number of identities in the
            tiling, accounting for overlapping HSPs
  Example : 
  Returns : number of identical residue pairs
  Args    :
 
 

conserved

  Title   : conserved
  Alias   : num_conserved
  Usage   : $num_conserved = $tiling->conserved()
  Function: Return the estimated or exact number of conserved sites in the 
            tiling, accounting for overlapping HSPs
  Example : 
  Returns : number of conserved residue pairs
  Args    :
 
 

length

  Title   : length
  Usage   : $max_length = $tiling->length($type)
  Function: Return the total number of residues of the subject or query
            sequence covered by the tiling
  Returns : number of "logical" residues covered
  Args    : scalar $type, one of 'hit', 'subject', 'query'
 
 

frac_identical

  Title   : frac_identical
  Usage   : $tiling->frac_identical($type)
  Function: Return the fraction of sequence length consisting
            of identical pairs
  Returns : scalar float
  Args    : scalar $type, one of 'hit', 'subject', 'query'
  Note    : This method must take account of the $type coordinate
            system and the length reporting method (see STATISTICS
            METHODS above)
 
 

percent_identity

  Title   : percent_identity
  Usage   : $tiling->percent_identity($type)
  Function: Return the fraction of sequence length consisting
            of identical pairs as a percentage
  Returns : scalar float
  Args    : scalar $type, one of 'hit', 'subject', 'query'
 
 

frac_conserved

  Title   : frac_conserved
  Usage   : $tiling->frac_conserved($type)
  Function: Return the fraction of sequence length consisting
            of conserved pairs
  Returns : scalar float
  Args    : scalar $type, one of 'hit', 'subject', 'query'
  Note    : This method must take account of the $type coordinate
            system and the length reporting method (see STATISTICS
            METHODS above)
 
 

percent_conserved

  Title   : percent_conserved
  Usage   : $tiling->percent_conserved($type)
  Function: Return the fraction of sequence length consisting
            of conserved pairs as a percentage
  Returns : scalar float
  Args    : scalar $type, one of 'hit', 'subject', 'query'
 
 

frac_aligned

  Title   : frac_aligned
  Usage   : $tiling->frac_aligned($type)
  Function: Return the fraction of B<input> sequence length consisting
            that was aligned by the algorithm
  Returns : scalar float
  Args    : scalar $type, one of 'hit', 'subject', 'query'
  Note    : This method must take account of the $type coordinate
            system and the length reporting method (see STATISTICS
            METHODS above)
 
 

range

  Title   : range
  Usage   : $tiling->range($type)
  Function: Returns the extent of the longest tiling
            as ($min_coord, $max_coord)
  Returns : array of two scalar integers
  Args    : scalar $type, one of 'hit', 'subject', 'query'
 
 

TILING ITERATORS

next_tiling

  Title   : next_tiling
  Usage   : @hsps = $self->next_tiling($type);
  Function: Obtain a tiling of HSPs over the $type ('hit', 'subject',
            'query') sequence
  Example :
  Returns : an array of HSPI objects
  Args    : scalar $type: one of 'hit', 'subject', 'query', with
            'subject' an alias for 'hit'
 
 

rewind_tilings

  Title   : rewind_tilings
  Usage   : $self->rewind_tilings($type)
  Function: Reset the next_tilings($type) iterator
  Example :
  Returns : True on success
  Args    : scalar $type: one of 'hit', 'subject', 'query', with
            'subject' an alias for 'hit'
 
 

INFORMATIONAL ACCESSORS

algorithm

  Title   : algorithm
  Usage   : $tiling->algorithm
  Function: Retrieve the algorithm name associated with the 
            invocant's hit object
  Returns : scalar string 
  Args    :