NAME
Bio::Glite - G-language Genome Analysis Environment REST service interface module
SYNOPSIS
use Bio::Glite; # Imports G-language GAE module
$gb = load("ecoli.gbk"); # Creates G's instance as $gb
# At the same time, read in ecoli.gbk.
# Read the annotation and sequence
# information
# See DESCRIPTION for details
$gb->seq_info(); # Prints the basic sequence information.
$find_ori_ter($gb); # Give $gb as the first argument to
# most of the analysis functionsDESCRIPTION
The G-language GAE fully supports most sequence databases.
Stored annotation information:
LOCUS
$gb->{LOCUS}->{id} -accession number
$gb->{LOCUS}->{length} -length of sequence
$gb->{LOCUS}->{nucleotide} -type of sequence ex. DNA, RNA
$gb->{LOCUS}->{circular} -1 when the genome is circular.
otherwise 0
$gb->{LOCUS}->{type} -type of species ex. BCT, CON
$gb->{LOCUS}->{date} -date of accession
HEADER
$gb->{HEADER}
COMMENT
$gb->{COMMENT}
FEATURE
Each FEATURE is numbered(FEATURE1 .. FEATURE1172), and is a
hash structure that contains all the keys of Genbank.
In other words, in most cases, FEATURE$i's hash at least
contains informations listed below:
$gb->{FEATURE$i}->{start}
$gb->{FEATURE$i}->{end}
$gb->{FEATURE$i}->{direction}
$gb->{FEATURE$i}->{join}
$gb->{FEATURE$i}->{note}
$gb->{FEATURE$i}->{type} -CDS,gene,RNA,etc.
$gb->{FEATURE$i}->{feature} -same as $i
To analyze each FEATURE, write:
foreach my $feature ($gb->feature()){
print $gb->{$feature}->{type}, "\n";
}
In the same manner, to analyze all CDS, write:
foreach my $cds ($gb->cds()){
print $gb->{$cds}->{gene}, "\n";
}
Feature or gene information can also be accessed with CDS numbers:
$gb->{CDS$i}->{start}
or with locus_tags or gene names (for CDS, tRNA, and rRNA)
$gb->{thrL}->{start}
$gb->{b0001}->{start}
BASE COUNT
$gb->{BASE_COUNT}
SEQ
$gb->seq() -sequence data following "ORIGIN" Supported methods of G-language Genome Analysis Environment
$gb = new G("genome file")
Name: $gb = new G("genome file") - create a G instance
see "help load" for more information.load
Name: load - load genome databases
This funciton is used to load genome databases into memory.
First option is the filename of the database. Default format is
the GenBank database. Database format is guessed from the extensions.
(eg. .gbk => GenBank, .fasta => FASTA, .embl => EMBL)
There are also several sample bacterial genomes included in the system.
$eco = load("ecoli"); # Escherichia coli K12 MG1655 - NC_000913
$bsub = load("bsub"); # Bacillus subtilis - NC_000964
$mgen = load("mgen"); # Mycoplasma genitalium - NC_000908
$cyano = load("cyano"); # Synechococcus sp. - NC_005070
$pyro = load("pyro"); # Pyrococcus furiosus - NC_003413
Data can be automatically donwloaded from public databases using
Uniform Sequence Address (USA) keys.
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html
Currently supported database keys are:
swiss, genbank, genpept, embl, refseq
eg.
$gb = load("embl:xlrhodop");
$gb = load("genbank:AY063336")
$gb = load("swiss:ROA1_HUMAN")
Second option specifies detailed actions.
'no msg' suprresses all STDOUT messages printed
when loading a database, including the
copyright info and sequence statistics.
'no cache' suppresses the use of database caching.
By default, databases are cached for
optimized performance. (since v.1.6.4)
'force cache' rebuilds database cache.
'multiple locus' this option merges multiple loci in the
database and load the information
as G-language instance.
'bioperl' this option creates a G instance from
a bioperl object.
eg. $bp = $bp->next_seq(); # bioperl
$gb = load($bp, "bioperl"); # G
'longest ORF annotation' this option predicts genes with longest ORF
algorithm (longest frame from start codon
to stop codon, with more than 17 amino
acids) and annotates the sequence.
'glimmer annotation' this option predicts genes using glimmer2,
a gene prediction software for microbial
genomes available from TIGR.
http://www.tigr.org/softlab/
Local installation of glimmer2 and setting
of PATH environment value is required.
- following options require bioperl installation -
'Fasta' this option loads a Fasta format database.
'EMBL' this option loads a EMBL format database.
'swiss' this option loads a swiss format database.
'SCF' this option loads a SCF format database.
'PIR' this option loads a PIR format database.
'GCG' this option loads a GCG format database.
'raw' this option loads a raw format database.
'ace' this option loads a ace format database.
'net GenBank' this option loads a GenBank format database from
NCBI database. With this option, the first value to
pass to load() function will be the accession
number of the database.$gb->output()
Name: $gb->output() - output the G instance data to file
Description:
Given a filename and an option, outputs the G-language data object
to the specified file in a flat-file database of a given format.
The options are the same as those of new(). Default format is 'GenBank'.
eg. $gb->output("my_genome.embl", "EMBL");
$gb->output("my_genome.gbk"); # with GenBank you can ommit the option.complement
Name: complement - get the complementary nucleotide sequence
Description:
Given a sequence, returns its complement.
eg. complement('atgc'); # returns 'gcat'method_list
Name: method_list - get the list of availabel G-language GAE functions
Description:
Returns an array of available method names.
When 1 is supplied as an argument, returns an array of API-related
method names.
eg. @methods = method_list(); # contains more than 100 analysis functions
@APImethods = method_list(1); # contains around 50 API-related methods.translate
Name: translate - translate a nucleotide sequence to amino acid sequence
Description:
Given a sequence, returns its translated sequence.
Regular codon table is used.
eg. translate('ctggtg'); # returns 'LV'$gb->seq()
Name: $gb->seq() - get the sequence data from G instance
Description:
Returns the entire sequence. Same as $gb->{SEQ};$gb->seq_info()
Name: $gb->seq_info() - display basic statistics about the data
Description:
Prints the basic information of the genome to STDOUT.$gb->find()
Name: $gb->find() - search through the genome data object with keywords
Description:
This method provides powerful means to search within the G-language genome
data object with keywords. Given a set of keywords, this method returns
the list of feature IDs corresponding to the search query. In G-language Shell,
search results are also directly printed out (you can specify -print=>1 option
in API mode to print within your program).
eg. @features = $gb->find('RNA', 'tyrosine'); # multiple keywords are allowed.
Keywords can be specific to each of the feature attributes:
eg. $gb->find(-type=>'CDS', -product=>'metabolism', 'subunit');
Regular expressions are allowed for keywords:
eg. $gb->find(-type=>'CDS', -EC_number=>'^2.7.');$gb->getseq()
Name: $gb->getseq() - get nucleotide sequence of the given positions (Perl coordinates)
Description:
Given the start and end positions (starting from 0 as in Perl),
returns the sequence specified.
eg. $gb->getseq(1,3); # returns the 2nd, 3rd, and 4th nucleotides.
Options:
-circular when the first position is larger than the second position,
retrieves the sequece spanning across the end of the circular
chromosome. (ex: $gb->getseq(4639670, 5, -circular))$gb->get_gbkseq()
Name: $gb->get_gbkseq() - get nucleotide sequence of the given positions (GenBank coordinates)
Description:
Given the start and end positions (starting from 1 as in
Genbank), returns the sequence specified.
eg. $gb->get_gbkseq(1,3); # returns the 1st, 2nd, and 3rd nucleotides.
Options:
-circular when the first position is larger than the second position,
retrieves the sequece spanning across the end of the circular
chromosome. (ex: $gb->getseq(4639670, 5, -circular))$gb->get_cdsseq()
Name: $gb->get_cdsseq() - get nucleotide sequence of the given CDS
Description:
Given a CDS ID, returns the CDS sequence.
'complement' is properly parsed.
eg. $gb->get_cdsseq('CDS1'); # returns the 'CDS1' sequence.$gb->get_geneseq()
Name: $gb->get_geneseq() - get nucleotide sequence of the given gene
Description:
Given a CDS ID, returns the CDS sequence, or the exon sequence
If introns are present.
'complement' is properly parsed, and introns are spliced out.
eg. $gb->get_geneseq('CDS1'); # returns the 'CDS1' sequence or exon.$gb->feature()
Name: $gb->feature() - get a list of feature IDs
Description:
Returns the array of all feature IDs.
Features are ignored when $gb->{$feature}->{on} is 0.
eg.
foreach ($gb->feature()){
$gb->get_cdsseq($_);
}
#prints all feature sequences.
Optionally, feature type can be supplied to return only the
specifies features.
eg. $gb->feature("tRNA"); # returns feature IDs only for tRNAs
Option of "all" always returns all features regardless of the
value of $gb->{$feature}->{on}.$gb->cds()
Name: $gb->cds() - get a list of CDS IDs
Description:
Returns the array of all feature IDs of CDS.
Features are ignored when $gb->{FEATURE$i}->{on} OR
$gb->{CDS$i}->{on} is 0.
!CAUTION! the object name is actually the FEATURE ID,
to enable access to all feature values. However, most of the
time you do not need to be aware of this difference.
eg.
foreach ($gb->cds()){
$gb->get_geneseq($_);
}
#prints all gene sequences.
Option of "all" always returns all features regardless of the
value of $gb->{$feature}->{on}.$gb->tRNA()
Name: $gb->tRNA() - get a list of feature IDs of tRNAs
Description:
Returns the array of all feature IDs of tRNAs.$gb->rRNA()
Name: $gb->rRNA() - get a list of feature IDs of rRNAs
Description:
Returns the array of all feature IDs of rRNAs.$gb->intergenic()
Name: $gb->intergenic() - get a list of IDs of intergenic regions
Description:
Returns the array of all IDs of intergenic regions.
Here "intergenic region" is defined as the region in a genome
between coding and stable RNA genes. $gb->gene()
Name: $gb->gene() - get a list of feature IDs of genes
Description:
Returns the array of all feature IDs of genes.$gb->disable_pseudogenes()
Name: $gb->disable_pseudogenes() - turns all pseudogenes off
Description:
Turns off all pseudogenes by setting $genome->{$feature}->{on}
to 0 when $genome->{$feature}->{pseudo} is true.$gb->next_feature()
Name: $gb->next_feature() - get the next feature ID
Description:
Given a feature ID, returns the ID of the next feature.
Second argument can be used to specify the type of the
next feature.
eg. $gb->next_feature(FEATURE1234); # returns 'FEATURE1235'
$gb->next_feature(FEATURE1234, 'tRNA');
# returns next feature ID whose type is 'tRNA'$gb->next_cds()
Name: $gb->next_cds() - get the feature ID of next CDS
Description:
Given a feature ID, returns the ID of the next cds.
This is same as $gb->next_feature($featureID, 'CDS');$gb->previous_feature()
Name: $gb->previous_feature() - get the previous feature ID
Description:
Given a feature ID, returns the ID of the previous feature.
Second argument can be used to specify the type of the
next feature.
eg. $gb->previous_feature(FEATURE1234); # returns 'FEATURE1233'
$gb->previous_feature(FEATURE1234, 'tRNA');
# returns previous feature ID whose type is 'tRNA'$gb->previous_cds()
Name: $gb->previous_cds() - get the feature ID of previous CDS
Description:
Given a feature ID, returns the ID of the previous cds.
This is same as $gb->previous_feature($featureID, 'CDS');$gb->startcodon()
Name: $gb->startcodon() - get the start codon of the given CDS
Description:
Given a CDS ID, returns the start codon.
eg. $gb->startcodon("FEATURE$i"); # returns 'atg'$gb->stopcodon()
Name: $gb->stopcodon() - get the stop codon of the given CDS
Description:
Given a CDS ID, returns the stop codon.
eg. $gb->stopcodon("FEATURE$i"); # returns 'tag'$gb->before_startcodon()
Name: $gb->before_startcodon() - get the upstream sequence of the given CDS
Description:
Given a CDS ID and length, returns the sequence upstream of
start codon.
eg. $gb->before_startcodon('CDS1', 100);
# returns 100 bp sequence upstream of the start codon of 'CDS1'.
Options:
Second argument specifying the length of sequence to retrieve is
optional. (default: 100).$gb->after_startcodon()
Name: $gb->after_startcodon() - get the sequence downstream of start codon of the given CDS
Description:
Given a CDS ID and length, returns the sequence downstream of
start codon.
eg. $gb->after_startcodon('CDS1', 100);
# returns 100 bp sequence downstream of the start codon of 'CDS1'.
Options:
Second argument specifying the length of sequence to retrieve is
optional. (default: 100).$gb->before_stopcodon()
Name: $gb->before_stopcodon() - get the sequence upstream of stop codon of the given CDS
Description:
Given a CDS ID and length, returns the sequence upstream of
stop codon.
eg. $gb->before_stopcodon('CDS1', 100);
# returns 100 bp sequence upstream of the stop codon of 'CDS1'.
Options:
Second argument specifying the length of sequence to retrieve is
optional. (default: 100).$gb->after_stopcodon()
Name: $gb->after_stopcodon() - get the downstream sequence of the given CDS
Description:
Given a CDS ID and length, returns the sequence downstream of
stop codon.
eg. $gb->after_stopcodon('CDS1', 100);
# returns 100 bp sequence downstream of the stop codon of 'CDS1'.
Options:
Second argument specifying the length of sequence to retrieve is
optional. (default: 100).$gb->around_startcodon()
Name: $gb->around_startcodon() - get the sequence around the startcodon of the given CDS
Description:
Given a CDS ID, lengths before startcodon and after start codon,
returns the sequence around of start codon.
eg. $gb->around_startcodon('FEATURE5239', 100, 100);
# returns 100 bp sequence before and after the start codon of 'CDS1',
# including the start codon itself
Options:
Optional Fourth argument containing a string "without" returns only the sequence
before and after the start codon, and without the stat codon itself.
eg. $gb->around_startcodon('FEATURE5239', 100, 100, "without");$gb->around_stopcodon()
Name: $gb->around_stopcodon() - get the sequence around the stopcodon of the given CDS
Description:
Given a CDS ID, lengths before stopcodon and after stop codon,
returns the sequence around of stop codon.
eg. $gb->around_stopcodon('FEATURE5239', 100, 100);
# returns 100 bp sequence before and after the stop codon of 'CDS1',
# including the stop codon itself
Options:
Optional Fourth argument containing a string "without" returns only the sequence
before and after the stop codon, and without the stat codon itself.
eg. $gb->around_stopcodon('FEATURE5239', 100, 100, "without");$gb->get_exon()
Name: $gb->get_exon() - get a list of exon sequences of the given CDS
Description:
Given a CDS ID, returns the exon sequence.
'complement' is properly parsed, and introns are spliced out.
eg. $gb->get_exon('CDS1'); returns the 'CDS1' exon.$gb->get_intron()
Name: $gb->intron() - get a list of intron sequences of the given CDS
Description:
Given a CDS ID, returns the intron sequences as array of
sequences.
eg. $gb->get_intron('CDS1');
# returns ($1st_intron, $2nd_intron,..)$gb->pos2feature()
Name: $gb->pos2feature() - get a feature ID from position
Description:
Given a GenBank position (sequence starting from position 1)
returns the feature ID (ex. FEATURE123) of the feature at
the given position. If multiple features exist for the given
position, the first feature to appear is returned. Returns
NULL if no feature exists.
When two positions are specified, all features within given
range is returned as an array of feature IDs.$gb->pos2gene()
Name: $gb->pos2gene() - get a feature ID of CDS from position
Description:
Given a GenBank position (sequence starting from position 1)
returns the feature ID (ex. FEATURE123) of the gene at
the given position. If multiple genes exists for the given
position, the first gene to appear is returned. Returns
NULL if no gene exists.
When two positions are specified, all genes within given
range is returned as an array of feature IDs.$gb->gene2id()
Name: $gb->gene2id() - get a feature ID from canonical gene name
Description:
Given a GenBank gene name, returns the feature ID (ex. FEATURE123).
Returns NULL if no gene exists.$gb->next_locus()
Name: $gb->next_locus() - read the next locus and update the G instance
Description:
Reads the next locus.
the G instance is then updated.
eg.
do{
}while($gb->next_locus());
# Enables multiple loci analysis. $gb->clone()
Name: $gb->clone() - create a copy of the G instance
Description:
Returns cloned G instance, which is a new G instance with
identical data. $gb->del_key()
Name: $gb->del_key() - delete a data object from G instance
Description:
Given a object, deletes it from the G instance structure
eg. $gb->del_key('FEATURE1'); # deletes 'FEATURE1' hash$gb->reverse_strand()
Name: $gb->reverse_strand() - create a G instance on complementary DNA strand
Description:
Returns a G instance for the complementary DNA strand.
All information, including the sequence and feature annotations
is switched to reflect that of the complementary DNA strand.
In other words, gene order, direction of genes (either direct or
complement), and positions are reversed.
Usage:
$new = $gb->reverse_strand();$gb->relocate_origin()
Name: $gb->relocate_origin() - create a G instance starting at given position
Description:
Returns a G instance starting at given position, assuming circular
chromosome. All information, including the sequence and feature
annotations are moved. Note that the given position is Perl position
and NOT GenBank position. GenBank position -1 equals Perl position.
Usage:
$new = $gb->relocate_origin($position);
This method would probably be most useful in conjunction with
find_ori_ter(), to create a G instance starting from the
origin of replication, as follows:
($ori, $ter) = find_ori_ter($gb);
$new = $gb->relocate_origin($ori);
Several of related methods can be concatenated. For example,
to create a GenBank file of complementary DNA strand starting
from the origin of replication, do the following:
$gb->reverse_strand()->relocate_origin($ori)->output("out.gbk");AUTHOR
Kazuharu Arakawa, gaou@sfc.keio.ac.jp