The G-language GAE fully supports most sequence databases.
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.
To analyze each FEATURE, write:
$i = 1;
while(defined(%{$gb->{FEATURE$i}})){
$i ++;
}
Each CDS is stored in a similar manner.
There are
$gb->{CDS$i}->{start}
$gb->{CDS$i}->{end}
$gb->{CDS$i}->{direction}
$gb->{CDS$i}->{join}
$gb->{CDS$i}->{feature} -number $n for $gb->{FEATURE$n}
where "CDS$i" = "FEATURE$n"
In the same manner, to analyze all CDS, write:
$i = 1;
while(defined(%{$gb->{CDS$i}})){
$i ++;
}
BASE COUNT
$gb->{BASE_COUNT}
SEQ
$gb->{SEQ} -sequence data following "ORIGIN"
new()
Creates a G instance.
First option is the filename of the database. Default format is
the GenBank database.
Second option specifies detailed actions.
'without annotation' this option skips the annotation.
'multiple locus' this option merges multiple loci in the
database and load the information
as G-language instance.
'long sequence' this option uses a pointer of the filehandle
to read the genome sequence. See
next_seq() method below for details.
'bioperl' this option creates a G instance from
a bioperl object.
eg. $bp = $bp->next_seq(); # bioperl
$gb = new G($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 new() function will be the accession
number of the database.
output()
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()
Given a sequence, returns its complement.
eg. complement('atgc'); returns 'gcat'
translate()
Given a sequence, returns its translated sequence.
Regular codon table is used.
eg. translate('ctggtg'); returns 'LV'
$gb->seq_info()
Prints the basic information of the genome to STDOUT.
$gb->DESTROY()
Destroys the G instance
$gb->del_key()
Given a object, deletes it from the G instance structure
eg. $gb->del_key('FEATURE1'); deletes 'FEATURE1' hash
$gb->getseq()
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.
$gb->get_gbkseq()
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.
$gb->get_cdsseq()
Given a CDS ID, returns the CDS sequence.
'complement' is properly parsed.
eg. $gb->get_cdsseq('CDS1'); returns the 'CDS1' sequence.
$gb->get_geneseq()
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.
$gb->feature()
Returns the array of all feature object name.
foreach ($gb->feature()){
$gb->get_cdsseq($_);
}
prints all feature sequences.
$gb->cds()
Returns the array of all cds object name.
!CAUTION! the object name is actually the FEATURE OBJECT NAME,
to enable access to all feature values. However, most of the
time you do not need to be aware of this difference.
foreach ($gb->cds()){
$gb->get_geneseq($_);
}
prints all gene sequences.
$gb->startcodon()
Given a CDS ID, returns the start codon.
eg. $gb->startcodon('CDS1'); returns 'atg'
$gb->stopcodon()
Given a CDS ID, returns the stop codon.
eg. $gb->stopcodon('CDS1'); returns 'tag'
$gb->before_startcodon()
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'.
$gb->after_startcodon()
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'.
$gb->before_stopcodon()
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'.
$gb->after_stopcodon()
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'.
$gb->get_intron()
Given a CDS ID, returns the intron sequences as array of
sequences.
eg. $gb->get_intron('CDS1');
returns ($1st_intron, $2nd_intron,..)
$gb->pos2feature()
Given a GenBank position (sequence starting from position 1)
returns the G-instance ID (ex. FEATURE123) of the feature at
the given position. If multiple features exists for the given
position, the first feature to appear is returned. Returns
NULL if no feature exists.
$gb->pos2gene()
Given a GenBank position (sequence starting from position 1)
returns the G-instance 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.
$gb->gene2id()
Given a GenBank gene name, returns the G object feature ID
(ex. FEATURE123). Returns NULL if no gene exists.
$gb->get_exon()
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.
$gb->next_locus()
Reads the next locus.
the G instance is then updated.
do{
}while($gb->next_locus());
Enables multiple loci analysis.
$gb->next_seq()
If G instance is created with 'long sequence' option,
$gb->next_seq() method replace the next chunk of sequence
to $gb->{SEQ}.
while($gb->next_seq(100000)){
print $gb->{SEQ};
}
Enables continuous analysis.
$gb->rewind_genome()
If G instance is created with 'long sequence' option,
$gb->rewind_genome() method puts the filehandle pointer back
to the ORIGIN position.
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