module Bio
bio.rb - Loading all BioRuby modules¶ ↑
- Copyright
-
Copyright © 2001-2007 Toshiaki Katayama <k@bioruby.org>
- License
-
The Ruby License
$Id:$
+
bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser¶ ↑
- Copyright
-
Copyright © 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 © 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 © 2008 Naohisa Goto <ng@bioruby.org>
- License
-
The Ruby License
bio/appl/blast/wublast.rb - WU-BLAST default output parser¶ ↑
- Copyright
-
Copyright © 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 © 2002, 2005 Toshiaki Katayama<k@bioruby.org>
- Copyright
-
Copyright © 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 © 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 © 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 © 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 © 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
¶ ↑
-
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 © 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 © 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
¶ ↑
-
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 © 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 © 2003 Mitsuteru C. Nakao <n@bioruby.org>
- License
-
The Ruby License
Example¶ ↑
References
¶ ↑
bio/appl/targetp/report.rb - TargetP
report class¶ ↑
- Copyright
-
Copyright © 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 © 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
¶ ↑
-
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 © 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 © 2001, 2005 Toshiaki Katayama <k@bioruby.org>
- License
-
The Ruby License
$Id:$
bio/data/codontable.rb - Codon Table¶ ↑
- Copyright
-
Copyright © 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 © 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 © 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 © 2001-2007 Toshiaki Katayama <k@bioruby.org>
- Copyright
-
Copyright © 2003 Masumi Itoh <m@bioruby.org>
- Copyright
-
Copyright © 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 © 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 © 2001 Mitsuteru C. Nakao <n@bioruby.org> Copyright © 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 © 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 © 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 © 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 © 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.
bio/location.rb - Locations/Location class (GenBank
location format)¶ ↑
- Copyright
-
Copyright © 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 © 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 © 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 © 2008 Naohisa Goto <ng@bioruby.org>,
- License
-
The Ruby License
bio/sequence/common.rb - common methods for biological sequence¶ ↑
- Copyright
-
Copyright © 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 © 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 © 2008 Naohisa Goto <ng@bioruby.org>
- License
-
The Ruby License
bio/sequence/generic.rb - generic sequence class to store an intact string¶ ↑
- Copyright
-
Copyright © 2006 Toshiaki Katayama <k@bioruby.org>
- License
-
The Ruby License
bio/sequence/na.rb - nucleic acid sequence class¶ ↑
- Copyright
-
Copyright © 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 © 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
¶ ↑
-
FASTQ format specification maq.sourceforge.net/fastq.shtml
bio/sequence/sequence_masker.rb - Sequence
masking helper methods¶ ↑
- Copyright
-
Copyright © 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/tree/output.rb - Phylogenetic tree formatter¶ ↑
- Copyright
-
Copyright © 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 © 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 © 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 © 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 ofBio::UniProtKB
. Please useBio::UniProtKB
.Bio::SPTR
may be deprecated in the future.- UniProt
Bio::UniProt
is changed to an alias ofBio::UniProtKB
. Please useBio::UniProtKB
.Bio::UniProt
may be deprecated in the future.Note that
Bio::SPTR
have been renamed toBio::UniProtKB
and is also an alias ofBio::UniProtKB
.