1Bio::Search::Hit::BlastUHsietr(3C)ontributed Perl DocumeBnitoa:t:iSoenarch::Hit::BlastHit(3)
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NAME

6       Bio::Search::Hit::BlastHit - Blast-specific subclass of
7       Bio::Search::Hit::GenericHit
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SYNOPSIS

10           use Bio::Search::Hit::BlastHit;
11           my $hit = new Bio::Search::Hit::BlastHit(-algorithm => 'blastp');
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13       # See Bio::Search::Hit::GenericHit for information about working with
14       Hits.
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16       # TODO: Describe how to configure a SearchIO stream so that it gener‐
17       ates #       GenericHit objects.
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DESCRIPTION

20       This object is a subclass of Bio::Search::Hit::GenericHit and provides
21       some operations that facilitate working with BLAST and PSI-BLAST Hits.
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23       For general information about working with Hits, see
24       Bio::Search::Hit::GenericHit.
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FEEDBACK

27       Mailing Lists
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29       User feedback is an integral part of the evolution of this and other
30       Bioperl modules. Send your comments and suggestions preferably to the
31       Bioperl mailing list.  Your participation is much appreciated.
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33         bioperl-l@bioperl.org                  - General discussion
34         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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36       Reporting Bugs
37
38       Report bugs to the Bioperl bug tracking system to help us keep track of
39       the bugs and their resolution. Bug reports can be submitted via the
40       web:
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42         http://bugzilla.open-bio.org/
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AUTHOR - Jason Stajich and Steve Chervitz

45       Email jason@bioperl.org Email sac@bioperl.org
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APPENDIX

48       The rest of the documentation details each of the object methods.
49       Internal methods are usually preceded with a _
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51       new
52
53        Title   : new
54        Usage   : my $obj = new Bio::Search::Hit::GenericHit();
55        Function: Builds a new Bio::Search::Hit::GenericHit object
56        Returns : Bio::Search::Hit::GenericHit
57        Args    : See Bio::Search::Hit::GenericHit() for other args.
58                  Here are the BLAST-specific args that can be used when
59                  creating BlastHit objects:
60                  -iteration    => integer for the PSI-Blast iteration number
61                  -found_again  => boolean, true if hit appears in a
62                                   "previously found" section of a PSI-Blast report.
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64       iteration
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66        Usage     : $hit->iteration( $iteration_num );
67        Purpose   : Gets the iteration number in which the Hit was found.
68        Example   : $iteration_num = $sbjct->iteration();
69        Returns   : Integer greater than or equal to 1
70                    Non-PSI-BLAST reports will report iteration as 1, but this number
71                    is only meaningful for PSI-BLAST reports.
72        Argument  : iteration_num (optional, used when setting only)
73        Throws    : none
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75       See Also   : found_again()
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77       found_again
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79        Title     : found_again
80        Usage     : $hit->found_again;
81                    $hit->found_again(1);
82        Purpose   : Gets a boolean indicator whether or not the hit has
83                    been found in a previous iteration.
84                    This is only applicable to PSI-BLAST reports.
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86                     This method indicates if the hit was reported in the
87                     "Sequences used in model and found again" section of the
88                     PSI-BLAST report or if it was reported in the
89                     "Sequences not found previously or not previously below threshold"
90                     section of the PSI-BLAST report. Only for hits in iteration > 1.
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92        Example   : if( $hit->found_again()) { ... };
93        Returns   : Boolean, true (1) if the hit has been found in a
94                    previous PSI-BLAST iteration.
95                    Returns false (0 or undef) for hits that have not occurred in a
96                    previous PSI-BLAST iteration.
97        Argument  : Boolean (1 or 0). Only used for setting.
98        Throws    : none
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100       See Also   : iteration()
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104perl v5.8.8                       2007-05-07     Bio::Search::Hit::BlastHit(3)