Mailing Lists¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

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¶

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

STATISTICS METHODS¶

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'

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'

algorithm¶

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