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`¶ ↑

meme.sdsc.edu/meme/intro.html

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`¶ ↑

www.drive5.com/muscle/
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.
Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113, 2004.

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`¶ ↑

probcons.stanford.edu/
Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340, 2005.

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`¶ ↑

Florea, L., et al., A Computer program for aligning a cDNA sequence with a genomic DNA sequence, Genome Research, 8, 967–974, 1998. www.genome.org/cgi/content/abstract/8/9/967

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`¶ ↑

www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
Notredame, C., Higgins, D.G. and Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217, 2000.

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')

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`¶ ↑

FASTA format (WikiPedia) en.wikipedia.org/wiki/FASTA_format
Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml

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`¶ ↑

((<URL:deposit.pdb.org/cc_dict_tut.html>))
deposit.pdb.org/het_dictionary.txt

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

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.

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

Copyright

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¶ ↑

License: The Ruby License

Description¶ ↑

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

`References`¶ ↑

FASTQ format specification maq.sourceforge.net/fastq.shtml

bio/sequence/sequence_masker.rb - `Sequence` masking helper methods¶ ↑

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/tree/output.rb - Phylogenetic tree formatter¶ ↑

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>
License: The Ruby License

$Id:$

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

Author: Trevor Wennblom <trevor@corevx.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>
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>
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>
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>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.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>
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>
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>
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>
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>
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>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.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>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.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>
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>
License: The Ruby License

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

License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.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.
“.pre: Pre-release version.

References: guides.rubygems.org/patterns/#prerelease-gems

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.

module Bio

bio.rb - Loading all BioRuby modules¶ ↑

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

Acknowledgements¶ ↑

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

Note¶ ↑

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

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

Description¶ ↑

bio/appl/emboss.rb - EMBOSS wrapper¶ ↑

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

About Bio::GCG::Seq¶ ↑

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

Report classes for the iprscan program.¶ ↑

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

Description¶ ↑

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

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

About Bio::Phylip::PhylipFormat¶ ↑

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

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

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

Example¶ ↑

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

Description¶ ↑

Example¶ ↑

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

bio/compat/references.rb - Obsoleted References class¶ ↑

Description¶ ↑

bio/data/aa.rb - Amino Acids¶ ↑

bio/data/codontable.rb - Codon Table¶ ↑

Data source¶ ↑

Examples¶ ↑

bio/data/na.rb - Nucleic Acids¶ ↑

Synopsis¶ ↑

Usage¶ ↑

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

Description¶ ↑

Examples¶ ↑

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

Description¶ ↑

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

KEGG GENES parser¶ ↑

Examples¶ ↑

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

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

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

About Bio::PDB::ChemicalComponent¶ ↑

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

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

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

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

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

bio/sequence.rb - biological sequence class¶ ↑

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

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

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

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

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

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

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

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

Description¶ ↑

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

Description¶ ↑

bio/tree/output.rb - Phylogenetic tree formatter¶ ↑

Description¶ ↑

bio/version.rb - BioRuby version information¶ ↑

bio/appl/emboss.rb - `EMBOSS` wrapper¶ ↑

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

About `Bio::GCG::Seq`¶ ↑

About `Bio::Phylip::PhylipFormat`¶ ↑

bio/appl/sosui/report.rb - `SOSUI` report class¶ ↑

bio/appl/targetp/report.rb - `TargetP` report class¶ ↑

bio/compat/references.rb - Obsoleted `References` class¶ ↑

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

`KEGG` GENES parser¶ ↑

bio/db/kegg/keggtab.rb - `KEGG` keggtab class¶ ↑

bio/db/pdb/chain.rb - chain class for `PDB`¶ ↑

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

About `Bio::PDB::ChemicalComponent`¶ ↑

bio/db/pdb/model.rb - model class for `PDB`¶ ↑

bio/db/pdb/residue.rb - residue class for `PDB`¶ ↑

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

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

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

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

bio/sequence/sequence_masker.rb - `Sequence` masking helper methods¶ ↑