Bio::Tools::SeqPattern.pm - Bioperl object for a sequence pattern or motif

Object Creation
use Bio::Tools::SeqPattern (); $pat1 = 'T[GA]AA...TAAT'; $pattern1 = new Bio::Tools::SeqPattern(-SEQ =>$pattern, -TYPE =>'Dna'); $pat2 = '[VILM]R(GXX){3,2}...[^PG]'; $pattern2 = new Bio::Tools::SeqPattern(-SEQ =>$pattern, -TYPE =>'Amino'); This module is included with the central Bioperl distribution: http://bio.perl.org/Core/Latest ftp://bio.perl.org/pub/DIST Follow the installation instructions included in the README file. The Bio::Tools::SeqPattern.pm module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"). Bio::Tools::SeqPattern.pm is a concrete class that inherits from Bio::Seq.pm. This class grew out of a need to have a standard module for doing routine tasks with sequence patterns such as: -- Forming a reverse-complement version of a nucleotide sequence pattern -- Expanding patterns containing ambiguity codes -- Checking for invalid regexp characters -- Untainting yet preserving special characters in the pattern Other features to look for in the future: -- Full pattern syntax checking -- Conversion between expanded and ondensed forms of the pattern A key motivation for Bio::Tools::SeqPattern.pm is to have a way to generate a reverse complement of a nucleotide sequence pattern. This makes possible simultaneous pattern matching on both sense and anti-sense strands of a query sequence. In principle, one could do such a search more inefficiently by testing ainst both sense and anti-sense versions of a sequence. It is entirely equivalent to test a regexp containing both sense and anti-sense versions of the *pattern* against one copy of the sequence. The latter approach is much more efficient since: 1) You need only one copy of the sequence. 2) Only one regexp is executed. 3) Regexp patterns are typically much smaller than sequences. Patterns can be quite complex and it is often difficult to generate the reverse complement pattern. The Bioperl SeqPattern.pm addresses this problem, providing a convenient set of tools for working with biological sequence regular expressions. Not all patterns have been tested. If you discover a pattern that is not handled properly by Bio::Tools::SeqPattern.pm, please send me some email (sac@genome.stanford.edu). Thanks.

Extended Alphabet Support
This module supports the same set of ambiguity codes for nucleotide sequences as supported by Bio::Seq.pm. These ambiguity codes define the behavior or the expand() method. Amino acid alphabet support is different from that of Seq.pm (see below). ------------------------------------------ Symbol Meaning Nucleic Acid ------------------------------------------ A A Adenine C C Cytosine G G Guanine T T Thymine U U Uracil M A or C R A or G Any purine W A or T S C or G Y C or T Any pyrimidine K G or T V A or C or G H A or C or T D A or G or T B C or G or T X G or A or T or C N G or A or T or C . G or A or T or C ------------------------------------------ Symbol Meaning ------------------------------------------ A Alanine C Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine P Proline Q Glutamine R Arginine S Serine T Threonine V Valine W Tryptophan Y Tyrosine B Any hydrophobic: IFVLWMAGCY Z Any hydrophilic: TSHEDQNKR X Any amino acid . Any amino acid

Multiple Format Support
Ultimately, this module should be able to build SeqPattern.pm objects objects using a variety of pattern formats such as ProSite, Blocks, Prints, GCG, etc. Currently, this module only supports patterns using a grep-like syntax. A simple demo script is included with the central Bioperl distribution (the INSTALLATION manpage) and is also available from: http://bio.perl.org/Core/Examples/seq_pattern.pl Bio::Root::Object.pm - Base class. Bio::Seq.pm - Lightweight sequence object. http://bio.perl.org/Projects/modules.html - Online module documentation http://bio.perl.org/ - Bioperl Project Homepage

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Steve A. Chervitz, sac@genome.stanford.edu See the the FEEDBACK manpage section for where to send bug reports and comments. Bio::Tools::SeqPattern.pm, 0.011 Copyright (c) 1997-8 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Title : new Usage : my $seqpat = new Bio::Tools::SeqPattern(); Purpose : Verifies that the type is correct for superclass (Bio::Seq.pm) : and calls superclass constructor last. Returns : n/a Argument : Parameters passed to new() Throws : Exception if the pattern string (seq) is empty. Comments : The process of creating a new SeqPattern.pm object : ensures that the pattern string is untained. See Also : the section on _untaint_pat(), Bio::Root::RootI::new(), Bio::Seq::_initialize() Title : alphabet_ok Usage : $mypat->alphabet_ok; Purpose : Checks for invalid regexp characters. : Overrides Bio::Seq::alphabet_ok() to allow : additional regexp characters ,.*()[]<>{}^$ : in addition to the standard genetic alphabet. : Also untaints the pattern and sets the sequence : object's sequence to the untained string. Returns : Boolean (1 | 0) Argument : n/a Throws : Exception if the pattern contains invalid characters. Comments : Does not call the superclass method. : Actaully permits any alphanumeric, not just the : standard genetic alphabet. See Also : Bio::Seq::alphabet_ok(), the section on _initialize() Title : expand Usage : $seqpat_object->expand(); Purpose : Expands the sequence pattern using special ambiguity codes. Example : $pat = $seq_pat->expand(); Returns : String containing fully expanded sequence pattern Argument : n/a Throws : Exception if sequence type is not recognized : (i.e., is not one of [DR]NA, Amino) See Also : Extended Alphabet Support, the section on _expand_pep(), the section on _exapand_nuc() Title : _expand_pep Usage : n/a; automatically called by expand() Purpose : Expands peptide patterns Returns : String (the expanded pattern) Argument : String (the unexpanded pattern) Throws : n/a See Also : the expand manpage(), the section on _expand_nuc() Title : _expand_nuc Purpose : Expands nucleotide patterns Returns : String (the expanded pattern) Argument : String (the unexpanded pattern) Throws : n/a See Also : the expand manpage(), the section on _expand_pep() Title : revcom Usage : revcom([1]); Purpose : Forms a pattern capable of recognizing the reverse complement : version of a nucleotide sequence pattern. Example : $pattern_object->revcom(); : $pattern_object->revcom(1); ## returns expanded rev complement pattern. Returns : Object reference for a new Bio::Tools::SeqPattern containing : the revcom of the current pattern as its sequence. Argument : (1) boolean (optional) (default= false) : true : expand the pattern before rev-complementing. : false: don't expand pattern before or after rev-complementing. Throws : Exception if called for amino acid sequence pattern. Comments : This method permits the simultaneous searching of both : sense and anti-sense versions of a nucleotide pattern : by means of a grep-type of functionality in which any : number of patterns may be or-ed into the recognition : pattern. : Overrides Bio::Seq::revcom() and calls it first thing. : The order of _fixpat() calls is critical. See Also : Bio::Seq::revcom(), the section on _fixpat_1(), the section on _fixpat_2(), the section on _fixpat_3(), the section on _fixpat_4(), the section on _fixpat_5() Title : _fixpat_1 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {7,5} --> {5,7} (Part I) : and [T^] --> [^T] (Part II) : and *N --> N* (Part III) Returns : String (the new, partially reversed pattern) Argument : String (the expanded pattern) Throws : n/a See Also : the revcom manpage() Title : _fixpat_2 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}Y ---> Y{5,7} : and {10,}. ---> .{10,} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : the revcom manpage() Title : _fixpat_3 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}(XXX) ---> (XXX){5,7} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : the revcom manpage() Title : _fixpat_4 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}[XXX] ---> [XXX]{5,7} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : the revcom manpage() Title : _fixpat_5 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all *[XXX] ---> [XXX]* : and *(XXX) ---> (XXX)* Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : the revcom manpage() Title : _fixpat_6 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all ?Y{5,7} ---> Y{5,7}? : and ?(XXX){5,7} ---> (XXX){5,7}? : and ?[XYZ]{5,7} ---> [XYZ]{5,7}? Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : the revcom manpage()

str
Title : str Usage : $obj->str($newval) Function: Returns : value of str Args : newvalue (optional)

type
Title : type Usage : $obj->type($newval) Function: Returns : value of type Args : newvalue (optional)

Data Members
Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind: All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!). It is easy for this documentation to become obsolete as this module is still evolving. Always double check this info and search for members not described here. An instance of Bio::Tools::RestrictionEnzyme.pm is a blessed reference to a hash containing all or some of the following fields: FIELD VALUE ------------------------------------------------------------------------ _rev : The corrected reverse complement of the fully expanded pattern. INHERITED DATA MEMBERS: _seq : (From Bio::Seq.pm) The original, unexpanded input sequence after untainting. _type : (From Bio::Seq.pm) 'Dna' or 'Amino'