Bio::Search::Tiling::TilingI(3pm) | User Contributed Perl Documentation | Bio::Search::Tiling::TilingI(3pm) |

# 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); }

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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 dataStatistics 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

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 :

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 :

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'

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)

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'

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)

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'

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)

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'

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'

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'

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

2017-08-30 | perl v5.26.0 |