This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/Tools/HMMER/Set, Next: Bio/Tools/IUPAC, Prev: Bio/Tools/HMMER/Results, Up: Module List Set of identical domains from HMMER matches ******************************************* NAME ==== Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches SYNOPSIS ======== # get a Set object probably from the results object print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n"; foreach $domain ( $set->each_Domain ) { print "Domain start ",$domain->start," end ",$domain->end,"\n"; } DESCRIPTION =========== Represents a set of HMMER domains hitting one sequence. HMMER reports two different scores, a per sequence total score (and evalue) and a per domain score and evalue. This object represents a collection of the same domain with the sequence bits score and evalue. (these attributes are also on the per domain scores, which you can get there). 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://www.bioperl.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@bioperl.org http://www.bioperl.org/bioperl-bugs/ AUTHOR - Ewan Birney ==================== Email birney@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ add_Domain ---------- Title : add_Domain Usage : $set->add_Domain($domain) Function: adds the domain to the list Returns : nothing Args : A Bio::Tools::HMMER::Domain object each_Domain ----------- Title : each_Domain Usage : foreach $domain ( $set->each_Domain() ) Function: returns an array of domain objects in this set Returns : array Args : none name ---- Title : name Usage : $obj->name($newval) Function: Example : Returns : value of name Args : newvalue (optional) evalue ------ Title : evalue Usage : $obj->evalue($newval) Function: Example : Returns : value of evalue Args : newvalue (optional)  File: pm.info, Node: Bio/Tools/IUPAC, Next: Bio/Tools/MZEF, Prev: Bio/Tools/HMMER/Set, Up: Module List Generates unique Seq objects from an ambiguous Seq object ********************************************************* NAME ==== IUPAC - Generates unique Seq objects from an ambiguous Seq object SYNOPSIS ======== use Bio::Seq; use Bio::Tools::IUPAC; my $ambiseq = new Bio::Seq (-seq => 'ARTCGUTGR', -type => 'Dna'); my $stream = new Bio::Tools::IUPAC(-seq => $ambiseq); while ($uniqueseq = $stream->next_seq()) { # process the unique Seq object. } DESCRIPTION =========== IUPAC is a tool that produces a stream of unique, "strict"-satisfying Seq objects from an ambiquous Seq object (containing non-standard characters given the meaning shown below) Extended Dna / Rna alphabet : (includes symbols for nucleotide ambiguity) ------------------------------------------ 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 W A or T S C or G Y C or T 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 IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE: Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030. ---------------------------------- Amino Acid alphabet: ------------------------------------------ Symbol Meaning ------------------------------------------ A Alanine B Aspartic Acid, Asparagine C Cystine 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 X Unknown Y Tyrosine Z Glutamic Acid, Glutamine * Terminator IUPAC-IUP AMINO ACID SYMBOLS: Biochem J. 1984 Apr 15; 219(2): 345-373 Eur J Biochem. 1993 Apr 1; 213(1): 2 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://www.bioperl.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@bioperl.org http://www.bioperl.org/bioperl-bugs/ AUTHOR - Aaron Mackey ===================== Email amackey@virginia.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new --- Title : new Usage : new Bio::Tools::IUPAC $seq; Function: returns a new seq stream (akin to SeqIO) Returns : a Bio::Tools::IUPAC stream object that will produce unique Seq objects on demand. Args : an ambiguously coded Seq.pm object that has a specified 'type' next_seq -------- Title : next_seq Usage : $iupac->next_seq() Function: returns the next unique Seq object Returns : a Seq.pm object Args : none.  File: pm.info, Node: Bio/Tools/MZEF, Next: Bio/Tools/OddCodes, Prev: Bio/Tools/IUPAC, Up: Module List Results of one MZEF run *********************** NAME ==== Bio::Tools::MZEF - Results of one MZEF run SYNOPSIS ======== $mzef = Bio::Tools::MZEF->new(-file => 'result.mzef'); # filehandle: $mzef = Bio::Tools::MZEF->new( -fh => \*INPUT ); # to indicate that the sequence was reversed prior to feeding it to MZEF # and that you want to have this reflected in the strand() attribute of # the exons, as well have the coordinates translated to the non-reversed # sequence $mzef = Bio::Tools::MZEF->new( -file => 'result.mzef', -strand => -1 ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same while($gene = $mzef->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # internal exons only @intrl_exons = $gene->exons('Internal'); # note that presently MZEF predicts only internal exons! } # essential if you gave a filename at initialization (otherwise the file # will stay open) $mzef->close(); DESCRIPTION =========== The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off *Note Bio/Tools/AnalysisResult: Bio/Tools/AnalysisResult, and therefore implements *Note Bio/SeqAnalysisParserI: Bio/SeqAnalysisParserI,. 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 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/ AUTHOR - Hilmar Lapp ==================== Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com) Describe contact details here APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ analysis_method --------------- Usage : $mzef->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /mzef/i. Returns : String Argument : n/a next_feature ------------ Title : next_feature Usage : while($gene = $mzef->next_feature()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : next_prediction --------------- Title : next_prediction Usage : while($gene = $mzef->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : _parse_predictions ------------------ Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : _prediction ----------- Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : _add_prediction --------------- Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : _predictions_parsed ------------------- Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE  File: pm.info, Node: Bio/Tools/OddCodes, Next: Bio/Tools/Prediction/Exon, Prev: Bio/Tools/MZEF, Up: Module List Object holding alternative alphabet coding for one protein sequence ******************************************************************** NAME ==== Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence SYNOPSIS ======== Take a sequence object from eg, an inputstream, and creates an object for the purposes of rewriting that sequence in another alphabet. These are abbreviated amino acid sequence alphabets, designed to simplify the statistical aspects of analysing protein sequences, by reducing the combinatorial explosion of the 20-letter alphabet. These abbreviated alphabets range in size from 2 to 8. Creating the OddCodes object, eg: my $inputstream = Bio::SeqIO->new( '-file' => "seqfile", '-format' => 'Fasta'); my $seqobj = $inputstream->next_seq(); my $oddcode_obj = Bio::Tools::Oddcodes->new(-seq => $seqobj); or: my $seqobj = Bio::PrimarySeq->new (-seq=>'[cut and paste a sequence here]', -moltype = 'protein', -id = 'test'); my $oddcode_obj = Bio::Tools::OddCodes->new(-seq => $seqobj); do the alternative coding, returning the answer as a reference to a string my $output = $oddcode_obj->structural(); my $output = $oddcode_obj->chemical(); my $output = $oddcode_obj->functional(); my $output = $oddcode_obj->charge(); my $output = $oddcode_obj->hydrophobic(); my $output = $oddcode_obj->Dayhoff(); my $output = $oddcode_obj->Sneath(); my $output = $oddcode_obj->Stanfel(); display sequence in new form, eg: my $new_coding = $$output; print "\n$new_coding"; DESCRIPTION =========== Bio::Tools::Oddcodes is a welterweight object for rewriting a protein sequence in an alternative alphabet. 8 of these are provided, ranging from the the 2-letter hydrophobic alphabet, to the 8-letter chemical alphabet. These are useful for the statistical analysis of protein sequences since they can partially avoid the combinatorial explosion produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers etc.) See Synopsis above for object creation code. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://www.bioperl.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@bioperl.org http://www.bioperl.org/bioperl-bugs/ AUTHOR ====== Derek Gatherer APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ structural ---------- Title : structural Usage : $output = $oddcode_obj->structural(); Function: turns amino acid sequence into 3-letter structural alphabet : A (ambivalent), E (external), I (internal) Example : a sequence ACDEFGH will become AAEEIAE Returns : Reference to the new sequence string Args : none functional ---------- Title : functional Usage : $output = $oddcode_obj->functional(); Function: turns amino acid sequence into 4-letter functional alphabet : A (acidic), C (basic), H (hydrophobic), P (polar) Example : a sequence ACDEFGH will become HPAAHHC Returns : Reference to the new sequence string Args : none hydrophobic ----------- Title : hydrophobic Usage : $output = $oddcode_obj->hydrophobic(); Function: turns amino acid sequence into 2-letter hydrophobicity alphabet : O (hydrophobic), I (hydrophilic) Example : a sequence ACDEFGH will become OIIIOII Returns : Reference to the new sequence string Args : none Dayhoff ------- Title : Dayhoff Usage : $output = $oddcode_obj->Dayhoff(); Function: turns amino acid sequence into 6-letter Dayhoff alphabet Example : a sequence ACDEFGH will become CADDGCE Returns : Reference to the new sequence string Args : none Sneath ------ Title : Sneath Usage : $output = $oddcode_obj->Sneath(); Function: turns amino acid sequence into 7-letter Sneath alphabet Example : a sequence ACDEFGH will become CEFFHCF Returns : Reference to the new sequence string Args : none Stanfel ------- Title : Stanfel Usage : $output = $oddcode_obj->Stanfel(); Function: turns amino acid sequence into 4-letter Stanfel alphabet Example : a sequence ACDEFGH will become AACCDAE Returns : Reference to the new sequence string Args : none chemical() ---------- Title : chemical Usage : $output = $oddcode_obj->chemical(); Function: turns amino acid sequence into 8-letter chemical alphabet : A (acidic), L (aliphatic), M (amide), R (aromatic) : C (basic), H (hydroxyl), I (imino), S (sulphur) Example : a sequence ACDEFGH will become LSAARAC Returns : Reference to the new sequence string Args : none charge ------ Title : charge Usage : $output = $oddcode_obj->charge(); Function: turns amino acid sequence into 3-letter charge alphabet Example : a sequence ACDEFGH will become NNAANNC Returns : Reference to the new sequence string Args : none  File: pm.info, Node: Bio/Tools/Prediction/Exon, Next: Bio/Tools/Prediction/Gene, Prev: Bio/Tools/OddCodes, Up: Module List A predicted exon feature ************************ NAME ==== Bio::Tools::Prediction::Exon - A predicted exon feature SYNOPSIS ======== See documentation of methods. DESCRIPTION =========== A feature representing a predicted exon. This class actually inherits off Bio::SeqFeature::Gene::Exon and therefore has all that functionality (also implements Bio::SeqFeatureI), plus a few methods supporting predicted features, like various scores and a significance. Even though these were inspired by GenScan results, at least a subset should be generally useable for exon prediction results. 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 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/ AUTHOR - Hilmar Lapp ==================== Email hlapp@gmx.net Describe contact details here APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ predicted_cds ------------- Title : predicted_cds Usage : $predicted_cds_dna = $exon->predicted_cds(); $exon->predicted_cds($predicted_cds_dna); Function: Get/Set the CDS (coding sequence) as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. predicted_protein ----------------- Title : predicted_protein Usage : $predicted_protein_seq = $exon->predicted_protein(); $exon->predicted_protein($predicted_protein_seq); Function: Get/Set the protein translation as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. significance ------------ Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : start_signal_score ------------------ Title : start_signal_score Usage : $sc = $obj->start_signal_score(); $obj->start_signal_score($evalue); Function: Get/Set a score for the exon start signal (acceptor splice site or initiation signal). Returns : Args : end_signal_score ---------------- Title : end_signal_score Usage : $sc = $obj->end_signal_score(); $obj->end_signal_score($evalue); Function: Get/Set a score for the exon end signal (donor splice site or termination signal). Returns : Args : coding_signal_score ------------------- Title : coding_signal_score Usage : $sc = $obj->coding_signal_score(); $obj->coding_signal_score($evalue); Function: Get/Set a score for the exon coding signal (e.g., coding potential). Returns : Args :  File: pm.info, Node: Bio/Tools/Prediction/Gene, Next: Bio/Tools/RestrictionEnzyme, Prev: Bio/Tools/Prediction/Exon, Up: Module List a predicted gene structure feature ********************************** NAME ==== Bio::Tools::Prediction::Gene - a predicted gene structure feature SYNOPSIS ======== See documentation of methods. DESCRIPTION =========== A feature representing a predicted gene structure. This class actually inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that functionality, plus a few methods supporting predicted sequence features, like a predicted CDS and a predicted translation. Exons held by an instance of this class will usually be instances of Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the documentation of the class that produced the instance. Normally, you will not want to create an instance of this class yourself. Instead, classes representing the results of gene structure prediction programs will do that. 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 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/ AUTHOR - Hilmar Lapp ==================== Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com Describe contact details here APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ predicted_cds ------------- Title : predicted_cds Usage : $predicted_cds_dna = $gene->predicted_cds(); $gene->predicted_cds($predicted_cds_dna); Function: Get/Set the CDS (coding sequence) as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. predicted_protein ----------------- Title : predicted_protein Usage : $predicted_protein_seq = $gene->predicted_protein(); $gene->predicted_protein($predicted_protein_seq); Function: Get/Set the protein translation as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.  File: pm.info, Node: Bio/Tools/RestrictionEnzyme, Next: Bio/Tools/Run/Alignment/Clustalw, Prev: Bio/Tools/Prediction/Gene, Up: Module List Bioperl object for a restriction endonuclease object. ***************************************************** NAME ==== Bio::Tools::RestrictionEnzyme.pm - Bioperl object for a restriction endonuclease object. SYNOPSIS ======== Object Creation --------------- require Bio::Tools::RestrictionEnzyme; ## Create a new object by name. $re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI'); ## Create a new object using special syntax ## which specifies the enzyme name, recognition site, and cut position. ## Used for enzymes not known to this module. $re2 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRV--GAT^ATC', -MAKE =>'custom'); INSTALLATION ============ 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. DESCRIPTION =========== The Bio::Tools::RestrictionEnzyme.pm module encapsulates generic data and methods for using restriction endonucleases for in silico restriction analysis of DNA sequences. Considerations -------------- This module is a precursor for a more full featured version that may do such things as download data from online databases such as REBase http://www.neb.com/rebase/. Thus, there is currently no functionality for obtaining data about commercial availability for a restriction enzyme. At some point in the future, it may be best to derive RestrictionEnzymes from a class such as Bio::Enzyme.pm or Bio::Prot::Protein.pm so that more data about the enzyme and related information can be easily obtained. This module is currently in use at http://genome-www.stanford.edu/Sacch3D/analysis/ *This module is at an early stage of development and is not yet ready for general use. API documentation is presently incomplete.* DEPENDENCIES ============ Bio::Tools::RestrictionEnzyme.pm is a concrete class that inherits from *Bio::Root::Object.pm* and uses by delegation *Bio::Seq.pm*. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - 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/ AUTHOR ====== Steve A. Chervitz, sac@genome.stanford.edu VERSION ======= Bio::Tools::RestrictionEnzyme.pm, 0.04 COPYRIGHT ========= 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. SEE ALSO ======== 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/Projects/Blast/ - Bioperl Blast Project http://bio.perl.org/ - Bioperl Project Homepage APPENDIX ======== Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. new === Title : new Purpose : Initializes the RestrictionEnzyme object and calls : superclass constructor last (Bio:Seq.pm). Returns : n/a Argument : Parameters passed to new() Comments : The process of creating a new SeqPattern.pm object : ensures that the pattern string is untained. See Also : `_make_custom' in this node(), `_make_standard' in this node(), *Bio::Seq.pm::_initialize()* _make_standard ============== Title : _make_standard Usage : n/a; automatically called by _initialize() Purpose : Permits custom RE object construction from name. : 'EcoRI'. Returns : Hash containing named parameters for Bio::Seq.pm constructor. Argument : String containing string with special syntax. Throws : Exception if the requested enzyme name is unavailable. : NOTE: Case sensitive. See Also : `_initialize' in this node(), `_make_custom' in this node() _make_custom ============ Title : _make_custom Usage : n/a; automatically called by _initialize() Purpose : Permits custom RE object construction from strings : such as 'EcoRI--G^AATTC' as the name of the enzyme. Returns : Hash containing named parameters for Bio::Seq.pm constructor. Argument : String containing string with special syntax. Throws : Exception if the string has bad syntax. : Warning if the string did not specify cut position. : Places cut site after 5'-most position. See Also : `_initialize' in this node() cuts_after ========== Title : cuts_after Usage : $re->cuts_after(); Purpose : Sets/Gets the position of cleavage relative to the 5' end. Example : $num = $re->cuts_after() Returns : Integer Argument : Integer (optional) Throws : Exception if argument is non-numeric. Access : Public Comments : This method is only needed to change the cuts at : position. This data is automatically set during : construction. See Also : `_make_standard' in this node(), `_make_custom' in this node() site ==== Title : site Usage : $re->site(); Purpose : Gets the recognition sequence for the enzyme. Example : $seq_string = $re->site(); Returns : String containing recognition sequence indicating : cleavage site as in 'G^AATTC'. Argument : n/a Throws : n/a seq === Title : seq Usage : $re->seq(); Purpose : Get the Bio::Seq.pm-derived object representing : the recognition sequence Returns : String Argument : n/a Throws : n/a See Also : `string' in this node(), `revcom' in this node() string ====== Title : string Usage : $re->string(); Purpose : Get a string representing the recognition sequence. Returns : String Argument : n/a Throws : n/a Comments : Delegates to the Bio::Seq.pm-derived object. See Also : `seq' in this node(), `revcom' in this node() revcom ====== Title : revcom Usage : $re->revcom(); Purpose : Get a string representing the reverse complement of : the recognition sequence. Returns : String Argument : n/a Throws : n/a Comments : Delegates to the Bio::Seq.pm-derived object, but needs to get out the string from it, as now Bio::Seq->revcom makes a Bio::Seq object See Also : `seq' in this node(), `string' in this node() cut_seq ======= Title : cut_seq Usage : $re->cut_seq(); Purpose : Conceptually cut or "digest" a DNA sequence with the given enzyme. Example : $string = $re->cut_seq(); Returns : List of strings containing the resulting fragments. Argument : Reference to a Bio::Seq.pm-derived object. Throws : Exception if argument is not an object. : (Does not yet verify that it is derived from Bio::Seq.pm.) Comments : Strategy relies on Perl's built-in split() function. : Since split removes the recognition pattern, the resulting : fragments must be repaired after split()-ing. : There is currently no support for partial digestions. cut_locations ============= Title : cut_locations Usage : my $locations = $re->cut_locations(); Purpose : Report the location of the recognition site(s) within : an input sequence. Example : my $locations = $re->annotate_seq($seqObj); Returns : Arrayref of starting locations where enzyme would cut Argument : Reference to a Bio::SeqI-derived sequence object. Throws : n/a Comments : annotate_seq ============ Title : annotate_seq Usage : $re->annotate_seq(); Purpose : Identify the location of the recognition site(s) within : an input sequence. Uses HTML. Example : $annot_seq = $re->annotate_seq($seqObj); Returns : String containing the annotated sequence. Argument : Reference to a Bio::Seq.pm-derived sequence object. Throws : n/a Comments : The annotated sequence must be viewed with a web : browser to see the location(s) of the recognition site(s). palindromic =========== Title : palindromic Usage : $re->palindromic(); Purpose : Determines if the recognition sequence is palindromic : for the current restriction enzyme. Returns : Boolean Argument : n/a Throws : n/a Access : Public Comments : A palindromic site (EcoRI): 5-GAATTC-3 : 3-CTTAAG-5 is_available ============ Title : is_available Usage : $re->is_available(); Purpose : Determine if an enzyme is available (to this module). : (see the package lexical %RE). Example : $re->is_available('EcoRI'); : &Bio::Tools::RestrictionEnzyme::is_available($object,'EcoRI'); Returns : Boolean Argument : String Throws : n/a Comments : This method does NOT give information about : commercial availability (yet). : Enzyme names are CASE SENSITIVE. See Also : `available_list' in this node() name ---- Title : name Usage : $obj->name($newval) Function: Example : Returns : value of name Args : newvalue (optional) available_list ============== Title : available_list Usage : $re->available_list([]); Purpose : Retrieve a list of currently available enzymes. Example : @all = $re->available_list(); ## All enzymes : @six_cutters = $re->available_list(6); ## All 6-cutters Returns : List of strings Argument : Integer (optional) Throws : n/a Comments : This method may be more appropriate for a REData.pm class. See Also : `is_available' in this node() FOR DEVELOPERS ONLY =================== 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: 1. Do NOT rely on these in any code outside of this module. 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!). 2. This documentation may be incomplete and out of date. 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 ------------------------------------------------------------------------ _seq : A Bio::Seq.pm-derived object. : _site : String containing the recognition sequence. : _cuts_after : Integer indicating the cleavage position relative to the : 5' end of the recognition sequence. INHERITED DATA MEMBERS: _name : (From Bio::Bio::Root::Object.pm) String containing name of the enzyme.  File: pm.info, Node: Bio/Tools/Run/Alignment/Clustalw, Next: Bio/Tools/Run/Alignment/TCoffee, Prev: Bio/Tools/RestrictionEnzyme, Up: Module List Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program ************************************************************************************************************************************** NAME ==== Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program SYNOPSIS ======== # Build a clustalw alignment factory @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); # Pass the factory a list of sequences to be aligned. $inputfilename = 't/cysprot.fa'; $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object. # or $seq_array_ref = \@seq_array; # where @seq_array is an array of Bio::Seq objects $aln = $factory->align($seq_array_ref); # Or one can pass the factory a pair of (sub)alignments #to be aligned against each other, e.g.: $aln = $factory->profile_align($aln1,$aln2); # where $aln1 and $aln2 are Bio::SimpleAlign objects. # Or one can pass the factory an alignment and one or more unaligned # sequences to be added to the alignment. For example: $aln = $factory->profile_align($aln1,$seq); # $seq is a Bio::Seq object. There are various additional options and input formats available. See the DESCRIPTION section that follows for additional details. DESCRIPTION =========== Note: this DESCRIPTION only documents the (Bio)perl interface to Clustalw. Clustalw, itself, is a large & complex program - for more information regarding clustalw, please see the clustalw documentation which accompanies the clustalw distribution. Clustalw is available from (among others) ftp://ftp.ebi.ac.uk/pub/software/. Clustalw.pm has been tested so far only under Linux. I expect that it should also work under other Unix systems. However, since the module is currently implemented using (unix) system calls, extensive modification may be necessary before Clustalw.pm would work under non-Unix operating systems (eg Windows, MacOS). Clustalw.pm has only been tested using version 1.8 of clustalw. Compatibility with earlier versions of the clustalw program is currently unknown. Before running Clustalw.pm successfully it will be necessary: to install clustalw on your system, to edit the variable $clustdir in Clustalw.pm to point to the clustalw program, and to ensure that users have execute privilieges for the clustalw program. Bio::Tools::Run::Alignment::Clustalw.pm: is an object for performing a multiple sequence alignment from a set of unaligned sequences and/or sub-alignments by means of the clustalw program. Initially, a clustalw "factory object" is created. Optionally, the factory may be passed most of the parameters or switches of the clustalw program, e.g.: @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); Any parameters not explicitly set will remain as the defaults of the clustalw program. Additional parameters and switches (not available in clustalw) may also be set. Currently, the only such parameter is "quiet", which when set to a non-zero value, suppresses clustalw terminal output. Not all clustalw parameters are supported at this stage. By default, Clustalw.pm output is returned solely in a the form of a BioPerl Bio::SimpleAlign object which can then be printed and/or saved in multiple formats using the AlignIO.pm module. Optionally the raw clustalw output file can be saved if the calling script specifies an output file (with the clustalw parameter OUTFILE). Currently only the GCG-MSF output file formats is supported. Other parameters and features (such as those corresponding to tree production) have not been implemented yet in Perl format. Alignment parameters can be changed and/or examined at any time after the factory has been created. The program checks that any parameter/switch being set/read is valid. However, currently no additional checks are included to check that parameters are of the proper type (eg string or numeric) or that their values are within the proper range. As an example, to change the value of the clustalw parameter ktuple to 3 and subsequently to check its value one would write: $ktuple = 3; $factory->ktuple($ktuple); $get_ktuple = $factory->ktuple(); Once the factory has been created and the appropriate parameters set, one can call the method align() to align a set of unaligned sequences, or call profile_align() to add one or more sequences or a second alignment to an initial alignment. Input to align() may consist of a set of unaligned sequences in the form of the name of file containing the sequences. For example, $inputfilename = 't/cysprot.fa'; $aln = $factory->align($inputfilename); Alternately one can create an array of Bio::Seq objects somehow $str = Bio::SeqIO->new(-file=> 't/cysprot.fa', '-format' => 'Fasta'); @seq_array =(); while ( my $seq = $str->next_seq() ) {push (@seq_array, $seq) ;} and pass the factory a reference to that array $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); In either case, align() returns a reference to a SimpleAlign object which can then be displayed, stored, or converted to a UnivAlign object for further manipulation. Once an initial alignment exists, one can pass the factory additional sequence(s) to be added (ie aligned) to the original alignment. The alignment can be passed as either an alignment file or a Bio:SimpleAlign object. The unaligned sequence(s) can be passed as a filename or as an array of BioPerl sequence objects or as a single BioPerl Seq object. For example (to add a single sequence to an alignment), $str = Bio::AlignIO->new(-file=> 't/cysprot1a.msf'); $aln = $str->next_aln(); $str1 = Bio::SeqIO->new(-file=> 't/cysprot1b.fa'); $seq = $str1->next_seq(); $aln = $factory->profile_align($aln,$seq); In either case, profile_align() returns a reference to a SimpleAlign object containing a new SimpleAlign object of the alignment with the additional sequence(s) added in. Finally one can pass the factory a pair of (sub)alignments to be aligned against each other. The alignments can be passed in the form of either a pair of alignment files or a pair of Bio:SimpleAlign objects. For example, $profile1 = 't/cysprot1a.msf'; $profile2 = 't/cysprot1b.msf'; $aln = $factory->profile_align($profile1,$profile2); or $str1 = Bio::AlignIO->new(-file=> 't/cysprot1a.msf'); $aln1 = $str1->next_aln(); $str2 = Bio::AlignIO->new(-file=> 't/cysprot1b.msf'); $aln2 = $str2->next_aln(); $aln = $factory->profile_align($aln1,$aln2); In either case, profile_align() returns a reference to a SimpleAlign object containing an (super)alignment of the two input alignments. For more examples of syntax and use of Clustalw.pm, the user is encouraged to run the script Clustalw.t is the bioperl/t directory. Note: Clustalw.pm is still under development. Various features of the clustalw program have not yet been implemented. If you would like that a specific clustalw feature be added to this perl interface, let me know. These can be specified as paramters when instantiating a new TCoffee object, or through get/set methods of the same name (lowercase). PARAMETER FOR ALIGNMENT COMPUTATION =================================== KTUPLE ------ Title : KTUPLE Description : (optional) set the word size to be used in the alignment This is the size of exactly matching fragment that is used. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity. For longer sequences (e.g. >1000 residues) you may need to increase the default TOPDIAGS -------- Title : TOPDIAGS Description : (optional) number of best diagonals to use The number of k-tuple matches on each diagonal (in an imaginary dot-matrix plot) is calculated. Only the best ones (with most matches) are used in the alignment. This parameter specifies how many. Decrease for speed; increase for sensitivity. WINDOW ------ Title : WINDOW Description : (optional) window size This is the number of diagonals around each of the 'best' diagonals that will be used. Decrease for speed; increase for sensitivity. PAIRGAP ------- Title : PAIRGAP Description : (optional) gap penalty for pairwise alignments This is a penalty for each gap in the fast alignments. It has little affect on the speed or sensitivity except for extreme values. FIXEDGAP -------- Title : FIXEDGAP Description : (optional) fixed length gap penalty FLOATGAP -------- Title : FLOATGAP Description : (optional) variable length gap penalty MATRIX ------ Title : MATRIX Default : PAM100 for DNA - PAM250 for protein alignment Description : (optional) substitution matrix used in the multiple alignments. Depends on the version of clustalw as to what default matrix will be used PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of weight matrices. The default for proteins in version 1.8 is the PAM series derived by Gonnet and colleagues. Note, a series is used! The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are. Different matrices work differently at each evolutionary distance. DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series) can be selected. The default is the matrix used by BESTFIT for comparison of nucleic acid sequences. TYPE ---- Title : TYPE Description : (optional) sequence type: protein or DNA. This allows you to explicitly overide the programs attempt at guessing the type of the sequence. It is only useful if you are using sequences with a VERY strange composition. OUTPUT ------ Title : OUTPUT Description : (optional) clustalw supports GCG or PHYLIP or PIR or Clustal format. See the Bio::AlignIO modules for which formats are supported by bioperl. OUTFILE ------- Title : OUTFILE Description : (optional) Name of clustalw output file. If not set module will erase output file. In any case alignment will be returned in the form of SimpleAlign objects TRANSMIT -------- Title : TRANSMIT Description : (optional) transitions not weighted. The default is to weight transitions as more favourable than other mismatches in DNA alignments. This switch makes all nucleotide mismatches equally weighted. 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 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/ AUTHOR - Peter Schattner ========================= Email schattner@alum.mit.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ exists_clustal() ---------------- Title : exists_clustal Usage : $clustalfound = Bio::Tools::Run::Alignment::Clustalw->exists_clustal() Function: Determine whether clustalw program can be found on current host Example : Returns : 1 if clustalw program found at expected location, 0 otherwise. Args : none align ----- Title : align Usage : $inputfilename = 't/cysprot.fa'; $aln = $factory->align($inputfilename); or $seq_array_ref = \@seq_array; @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); Function: Perform a multiple sequence alignment Example : Returns : Reference to a SimpleAlign object containing the sequence alignment. Args : Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array. profile_align ------------- Title : profile_align Usage : Function: Perform an alignment of 2 (sub)alignments Example : Returns : Reference to a SimpleAlign object containing the (super)alignment. Args : Names of 2 files containing the subalignments or references to 2 Bio::SimpleAlign objects. Throws an exception if arguments are not either strings (eg filenames) or references to SimpleAlign objects. _run ---- Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to clustalw program Example : Returns : nothing; clustalw output is written to a temporary file $TMPOUTFILE Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to clustalw _setinput() ----------- Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for clustalw program Example : Returns : name of file containing clustalw data input Args : Seq or Align object reference or input file name _setparams() ------------ Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for clustalw program Example : Returns : parameter string to be passed to clustalw during align or profile_align Args : name of calling object