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BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Search::Tiling::TilingI

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:

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 
          invocant's hit object
Returns : scalar string 
Args    :