module Bio

bio.rb - Loading all BioRuby modules

Copyright

Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

+

bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser

Copyright

Copyright (C) 2005 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.

Acknowledgements

Thanks to Tomoaki NISHIYAMA <tomoakin __at__ kenroku.kanazawa-u.ac.jp> for providing bl2seq parser patches based on lib/bio/appl/blast/format0.rb.

bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser

Copyright

Copyright (C) 2002, 2003, 2007 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

Note

This file is automatically loaded by bio/appl/blast/report.rb

bio/appl/blast/remote.rb - remote BLAST wrapper basic module

Copyright

Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

bio/appl/blast/wublast.rb - WU-BLAST default output parser

Copyright

Copyright (C) 2003, 2008 Naohisa GOTO <ng@bioruby.org>

License

The Ruby License

Description

WU-BLAST default output parser.

The parser is still incomplete and may contain many bugs, because I didn't have WU-BLAST license. It was tested under web-based WU-BLAST results and obsolete version downloaded from blast.wustl.edu/ .

References

bio/appl/emboss.rb - EMBOSS wrapper

Copyright

Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org>

Copyright

Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>

License

The Ruby License

$Id: emboss.rb,v 1.9 2008/01/10 03:51:06 ngoto Exp $

+

bio/appl/gcg/seq.rb - GCG sequence file format class (.seq/.pep file)

Copyright

Copyright (C) 2003, 2006 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

$Id: seq.rb,v 1.3 2007/04/05 23:35:39 trevor Exp $

About Bio::GCG::Seq

Please refer document of Bio::GCG::Seq.

bio/appl/iprscan/report.rb - a class for iprscan output.

Copyright

Copyright (C) 2006 Mitsuteru C. Nakao <mn@kazusa.or.jp>

License

The Ruby License

Report classes for the iprscan program.

bio/appl/meme/motif.rb - Class to represent a sequence motif

Copyright

Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>,

License

The Ruby License

Description

This file contains a minimal class to represent meme motifs

References

bio/appl/muscle.rb - MUSCLE application wrapper class

Copyright

Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

$Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $

Bio::Muscle is a wrapper class to execute MUSCLE.

References

bio/appl/phylip/alignment.rb - phylip multiple alignment format parser

Copyright

Copyright (C) 2006 GOTO Naohisa <ng@bioruby.org>

License

The Ruby License

$Id: alignment.rb,v 1.2 2007/04/05 23:35:40 trevor Exp $

About Bio::Phylip::PhylipFormat

Please refer document of Bio::Phylip::PhylipFormat class.

bio/appl/probcons.rb - ProbCons application wrapper class

Copyright

Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

$Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $

Bio::Probcons is a wrapper class to execute ProbCons (Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences).

References

bio/appl/sim4/report.rb - sim4 result parser

Copyright

Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>

License

The Ruby License

$Id:$

The sim4 report parser classes.

References

bio/appl/sosui/report.rb - SOSUI report class

Copyright

Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>

License

The Ruby License

Example

References

bio/appl/targetp/report.rb - TargetP report class

Copyright

Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>

License

The Ruby License

$Id:$

Description

TargetP class for www.cbs.dtu.dk/services/TargetP/

Example

References

bio/appl/tcoffee.rb - T-Coffee application wrapper class

Copyright

Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

$Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $

Bio::Tcoffee is a wrapper class to execute T-Coffee.

References

bio/compat/references.rb - Obsoleted References class

Copyright

Copyright (C) 2008 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jandot@bioruby.org>, Naohisa Goto <ng@bioruby.org>

License

The Ruby License

$Id: references.rb,v 1.1.2.1 2008/03/04 10:07:49 ngoto Exp $

Description

The Bio::References class was obsoleted after BioRuby 1.2.1. To keep compatibility, some wrapper methods are provided in this file. As the compatibility methods (and Bio::References) will soon be removed, Please change your code not to use Bio::References.

Note that Bio::Reference is different from Bio::References. Bio::Reference still exists for storing a reference information in sequence entries.

bio/data/aa.rb - Amino Acids

Copyright

Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

bio/data/codontable.rb - Codon Table

Copyright

Copyright (C) 2001, 2004 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

Data source

Data in this class is converted from the NCBI's genetic codes page.

* ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t>))

Examples

Obtain a codon table No.1 – Standard (Eukaryote)

table = Bio::CodonTable[1]

Obtain a copy of the codon table No.1 to modify. In this example, reassign a seleno cystein ('U') to the 'tga' codon.

table = Bio::CodonTable.copy(1)
table['tga'] = 'U'

Create a new codon table by your own from the Hash which contains pairs of codon and amino acid. You can also define the table name in the second argument.

hash = { 'ttt' => 'F', 'ttc' => 'ttc', ... }
table = Bio::CodonTable.new(hash, "my codon table")

Obtain a translated amino acid by codon.

table = Bio::CodonTable[1]
table['ttt']  # => F

Reverse translation of a amino acid into a list of relevant codons.

table = Bio::CodonTable[1]
table.revtrans("A")  # => ["gcg", "gct", "gca", "gcc"]

bio/data/na.rb - Nucleic Acids

Copyright

Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

Synopsis

Bio::NucleicAcid class contains data related to nucleic acids.

Usage

Examples:

require 'bio'

puts "### na = Bio::NucleicAcid.new"
na = Bio::NucleicAcid.new

puts "# na.to_re('yrwskmbdhvnatgc')"
p na.to_re('yrwskmbdhvnatgc')

puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')

puts "# na.weight('A')"
p na.weight('A')

puts "# Bio::NucleicAcid.weight('A')"
p Bio::NucleicAcid.weight('A')

puts "# na.weight('atgc')"
p na.weight('atgc')

puts "# Bio::NucleicAcid.weight('atgc')"
p Bio::NucleicAcid.weight('atgc')

TODO save on db reading from a genbank or embl object

require 'bio/sequence'

bio/db/fasta/defline.rb - FASTA defline parser class

Copyright

Copyright (C) 2001, 2002 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>, Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

Description

Bio::FastaDefline is a parser class for definition line (defline) of the FASTA format.

Examples

rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
rub.entry_id       ==> 'gi|671595'
rub.get('emb')     ==> 'CAA85678.1'
rub.emb            ==> 'CAA85678.1'
rub.gi             ==> '671595'
rub.accession      ==> 'CAA85678'
rub.accessions     ==> [ 'CAA85678' ]
rub.acc_version    ==> 'CAA85678.1'
rub.locus          ==> nil
rub.list_ids       ==> [["gi", "671595"],
                        ["emb", "CAA85678.1", nil],
                        ["Perovskia abrotanoides"]]

ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
ckr.entry_id      ==> "gi|2495000"
ckr.sp            ==> "CCKR_CAVPO"
ckr.pir           ==> "I51898"
ckr.gb            ==> "AAB29504.1"
ckr.gi            ==> "2495000"
ckr.accession     ==> "AAB29504"
ckr.accessions    ==> ["Q63931", "AAB29504"]
ckr.acc_version   ==> "AAB29504.1"
ckr.locus         ==> nil
ckr.description   ==>
  "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
ckr.descriptions  ==>
  ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
   "cholecystokinin A receptor - guinea pig",
   "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
ckr.words         ==> 
  ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
   "receptor", "type"]
ckr.id_strings    ==>
  ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
   "544724", "AAB29504.1", "Cavia"]
ckr.list_ids      ==>
  [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
   ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
   ["gb", "AAB29504.1", nil], ["Cavia"]]

References

bio/db/kegg/common.rb - Common methods for KEGG database classes

Copyright

Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>

Copyright

Copyright (C) 2003 Masumi Itoh <m@bioruby.org>

Copyright

Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp>

License

The Ruby License

Description

Note that the modules in this file are intended to be Bio::KEGG::* internal use only.

This file contains modules that implement methods commonly used from KEGG database parser classes.

bio/db/kegg/genes.rb - KEGG/GENES database class

Copyright

Copyright (C) 2001, 2002, 2006, 2010 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

KEGG GENES parser

See www.genome.jp/kegg/genes.html

Examples

require 'bio/io/fetch'
entry_string = Bio::Fetch.query('genes', 'b0002')

entry = Bio::KEGG::GENES.new(entry_string)

# ENTRY
p entry.entry       # => Hash

p entry.entry_id    # => String
p entry.division    # => String
p entry.organism    # => String

# NAME
p entry.name        # => String
p entry.names       # => Array

# DEFINITION
p entry.definition  # => String
p entry.eclinks     # => Array

# PATHWAY
p entry.pathway     # => String
p entry.pathways    # => Hash

# POSITION
p entry.position    # => String
p entry.chromosome  # => String
p entry.gbposition  # => String
p entry.locations   # => Bio::Locations

# MOTIF
p entry.motifs      # => Hash of Array

# DBLINKS
p entry.dblinks     # => Hash of Array

# STRUCTURE
p entry.structure   # => Array

# CODON_USAGE
p entry.codon_usage # => Hash
p entry.cu_list     # => Array

# AASEQ
p entry.aaseq       # => Bio::Sequence::AA
p entry.aalen       # => Fixnum

# NTSEQ
p entry.ntseq       # => Bio::Sequence::NA
p entry.naseq       # => Bio::Sequence::NA
p entry.ntlen       # => Fixnum
p entry.nalen       # => Fixnum

bio/db/kegg/keggtab.rb - KEGG keggtab class

Copyright

Copyright (C) 2001 Mitsuteru C. Nakao <n@bioruby.org> Copyright (C) 2003, 2006 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id: keggtab.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $

bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2007 Center for Biomedical Research Informatics, University of Minnesota (cbri.umn.edu)

License

The Ruby License

$Id:$

definition of the PDB class

bio/db/pdb/chain.rb - chain class for PDB

Copyright

Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::PDB::Chain

Please refer Bio::PDB::Chain.

bio/db/pdb/chemicalcomponent.rb - PDB Chemical Component Dictionary parser

Copyright

Copyright (C) 2006 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>

License

The Ruby License

About Bio::PDB::ChemicalComponent

Please refer Bio::PDB::ChemicalComponent.

References

bio/db/pdb/model.rb - model class for PDB

Copyright

Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::PDB::Model

Please refer Bio::PDB::Model.

bio/db/pdb/residue.rb - residue class for PDB

Copyright

Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::PDB::Residue

Bio::PDB::Heterogen

bio/db/soft.rb - Interface for SOFT formatted files

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

$Id:$

bio/feature.rb - Features/Feature class (GenBank Feature table)

Copyright

Copyright © 2002, 2005 Toshiaki Katayama <k@bioruby.org>

2006        Jan Aerts <jan.aerts@bbsrc.ac.uk>
License

The Ruby License

bio/io/flatfile.rb - flatfile access wrapper class

Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>
License

The Ruby License

$Id:$

Bio::FlatFile is a helper and wrapper class to read a biological data file. It acts like a IO object. It can automatically detect data format, and users do not need to tell the class what the data is.

Ok Hilmar gives to me some clarification 1) “EMBL/GenBank/SwissProt” name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.

If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.

TODO: 1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something “EMBL/GenBank/SwissProt” or contestualized. 2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file. 3) Chk Locations in Biofeatures ArSQL

bio/location.rb - Locations/Location class (GenBank location format)

Copyright

Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>

2006       Jan Aerts <jan.aerts@bbsrc.ac.uk>
2008       Naohisa Goto <ng@bioruby.org>
License

The Ruby License

$Id:$

bio/sequence.rb - biological sequence class

Copyright

Copyright (C) 2000-2006 Toshiaki Katayama <k@bioruby.org>, Yoshinori K. Okuji <okuji@enbug.org>, Naohisa Goto <ng@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jan.aerts@bbsrc.ac.uk>

License

The Ruby License

bio/sequence/aa.rb - amino acid sequence class

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>

License

The Ruby License

bio/sequence/adapter.rb - Bio::Sequence adapter helper module

Copyright

Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>,

License

The Ruby License

bio/sequence/common.rb - common methods for biological sequence

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>

License

The Ruby License

bio/sequence/compat.rb - methods for backward compatibility

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>

License

The Ruby License

bio/sequence/dblink.rb - sequence ID with database name

Copyright

Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

bio/sequence/generic.rb - generic sequence class to store an intact string

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

bio/sequence/na.rb - nucleic acid sequence class

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>

License

The Ruby License

bio/sequence/quality_score.rb - Sequence quality score manipulation modules

Copyright

Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Description

Sequence quality score manipulation modules, mainly used by Bio::Fastq and related classes.

References

bio/sequence/sequence_masker.rb - Sequence masking helper methods

Copyright

Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Description

Bio::Sequence::SequenceMasker is a mix-in module to provide helpful methods for masking a sequence.

For details, see documentation of Bio::Sequence::SequenceMasker.

bio/shell/plugin/keggdas.rb - plugin for KEGG DAS

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $

bio/tree/output.rb - Phylogenetic tree formatter

Copyright

Copyright (C) 2004-2006 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Description

This file contains formatter of Newick, NHX and Phylip distance matrix.

References

bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

$Id:$

bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

$Id:$

bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/dense_int_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange

Copyright

Copyright (C) 2011 Naohisa Goto <ng@bioruby.org> Tomoaki NISHIYAMA

License

The Ruby License

bio/util/restriction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/horizontal_cut_range.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/sequence_range/fragment.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/analysis/fragments.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/range/vertical_cut_range.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb - The cut locations, in enzyme notation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/util/restriction_enzyme/sorted_num_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange

Copyright

Copyright (C) 2011 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

bio/version.rb - BioRuby version information

Copyright

Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>, Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Constants

BIORUBY_EXTRA_VERSION

Extra version specifier (String or nil). Existance of the value indicates development version.

nil

Release version.

“-dev”

Development version (with YYYYMMDD digits).

“.20150630”

Development version (specify the date digits).

By default, if the third digit (teeny) of BIORUBY_VERSION is 0, the version is regarded as a development version.

BIORUBY_VERSION

BioRuby version (Array containing Integer)

BIORUBY_VERSION_ID

Version identifier, including extra version string (String) Unlike BIORUBY_VERSION, it is not comparable.

SPTR

Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future.

UniProt

Bio::UniProt is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future.

Note that Bio::SPTR have been renamed to Bio::UniProtKB and is also an alias of Bio::UniProtKB.