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Manual Reference Pages  -  BIO::SEARCH::TILING::TILINGI (3)

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NAME

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

CONTENTS

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:



  https://github.com/bioperl/bioperl-live/issues



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
           invocants hit object
 Returns : scalar string
 Args    :



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