Provided by: libboulder-perl_1.30-6_all 
NAME
Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones
SYNOPSIS
use Boulder::Genbank
# network access via Entrez
$gb = Boulder::Genbank->newFh( qw(M57939 M28274 L36028) );
while ($data = <$gb>) {
print $data->Accession;
@introns = $data->features->Intron;
print "There are ",scalar(@introns)," introns.\n";
$dna = $data->Sequence;
print "The dna is ",length($dna)," bp long.\n";
my @features = $data->features(-type=>[ qw(Exon Source Satellite) ],
-pos=>[90,310] );
foreach (@features) {
print $_->Type,"\n";
print $_->Position,"\n";
print $_->Gene,"\n";
}
}
# another syntax
$gb = new Boulder::Genbank(-accessor=>'Entrez',
-fetch => [qw/M57939 M28274 L36028/]);
# local access via Yank
$gb = new Boulder::Genbank(-accessor=>'Yank',
-fetch=>[qw/M57939 M28274 L36028/]);
while (my $s = $gb->get) {
# etc.
}
# parse a file of Genbank records
$gb = new Boulder::Genbank(-accessor=>'File',
-fetch => '/usr/local/db/gbpri3.seq');
while (my $s = $gb->get) {
# etc.
}
# parse flatfile records yourself
open (GB,"/usr/local/db/gbpri3.seq");
local $/ = "//\n";
while (<GB>) {
my $s = Boulder::Genbank->parse($_);
# etc.
}
DESCRIPTION
Boulder::Genbank provides retrieval and parsing services for NCBI Genbank-format records.
It returns Genbank entries in Stone format, allowing easy access to the various fields and
values. Boulder::Genbank is a descendent of Boulder::Stream, and provides a stream-like
interface to a series of Stone objects.
>> IMPORTANT NOTE <<
As of January 2002, NCBI has changed their Batch Entrez interface. I have modified
Boulder::Genbank so as to use a "demo" interface, which fixes things, but this isn't
guaranteed in the long run.
I have written to NCBI, and they may fix this -- or they may not.
>> IMPORTANT NOTE <<
Access to Genbank is provided by three different accessors, which together give access to
remote and local Genbank databases. When you create a new Boulder::Genbank stream, you
provide one of the three accessors, along with accessor-specific parameters that control
what entries to fetch. The three accessors are:
Entrez
This provides access to NetEntrez, accessing the most recent Genbank information
directly from NCBI's Web site. The parameters passed to this accessor are either a
series of Genbank accession numbers, or an Entrez query (see
http://www.ncbi.nlm.nih.gov/Entrez/linking.html). If you provide a list of accession
numbers, the stream will return a series of stones corresponding to the numbers.
Otherwise, if you provided an Entrez query, the entries returned will be in the order
returned by Entez.
File
This provides access to local Genbank entries by reading from a flat file (typically
one of the .seq files downloadable from NCBI's Web site). The stream will return a
Stone corresponding to each of the entries in the file, starting from the top of the
file and working downward. The parameter in this case is the path to the local file.
Yank
This provides access to local Genbank entries using Will Fitzhugh's Yank program.
Yank provides fast indexed access to a Genbank flat file using the accession number as
the key. The parameter passed to the Yank accessor is a list of accession numbers.
Stones will be returned in the requested order. By default the yank binary lives in
/usr/local/bin/yank. To support other locations, you may define the environment
variable YANK to contain the full path.
It is also possible to parse a single Genbank entry from a text string stored in a scalar
variable, returning a Stone object.
Boulder::Genbank methods
This section lists the public methods that the Boulder::Genbank class makes available.
new()
# Network fetch via Entrez, with accession numbers
$gb=new Boulder::Genbank(-accessor => 'Entrez',
-fetch => [qw/M57939 M28274 L36028/]);
# Same, but shorter and uses -> operator
$gb = Boulder::Genbank->new qw(M57939 M28274 L36028);
# Network fetch via Entrez, with a query
# Network fetch via Entrez, with a query
$query = 'Homo sapiens[Organism] AND EST[Keyword]';
$gb=new Boulder::Genbank(-accessor => 'Entrez',
-fetch => $query);
# Local fetch via Yank, with accession numbers
$gb=new Boulder::Genbank(-accessor => 'Yank',
-fetch => [qw/M57939 M28274 L36028/]);
# Local fetch via File
$gb=new Boulder::Genbank(-accessor => 'File',
-fetch => '/usr/local/genbank/gbpri3.seq');
The new() method creates a new Boulder::Genbank stream on the accessor provided. The
three possible accessors are Entrez, Yank and File. If successful, the method returns
the stream object. Otherwise it returns undef.
new() takes the following arguments:
-accessor Name of the accessor to use
-fetch Parameters to pass to the accessor
-proxy Path to an HTTP proxy, used when using
the Entrez accessor over a firewall.
Specify the accessor to use with the -accessor argument. If not specified, it
defaults to Entrez.
-fetch is an accessor-specific argument. The possibilities are:
For Entrez, the -fetch argument may point to a scalar, in which case it is interpreted
as an Entrez query string. See http://www.ncbi.nlm.nih.gov/Entrez/linking.html for a
description of the query syntax. Alternatively, -fetch may point to an array
reference, in which case it is interpreted as a list of accession numbers to retrieve.
If -fetch points to a hash, it is interpreted as extended information. See "Extended
Entrez Parameters" below.
For Yank, the -fetch argument must point to an array reference containing the
accession numbers to retrieve.
For File, the -fetch argument must point to a string-valued scalar, which will be
interpreted as the path to the file to read Genbank entries from.
For Entrez (and Entrez only) Boulder::Genbank allows you to use a shortcut syntax in
which you provde new() with a list of accession numbers:
$gb = new Boulder::Genbank('M57939','M28274','L36028');
newFh()
This works like new(), but returns a filehandle. To recover each GenBank record read
from the filehandle with the <> operator:
$fh = Boulder::GenBank->newFh('M57939','M28274','L36028');
while ($record = <$fh>) {
print $record->asString;
}
get()
The get() method is inherited from Boulder::Stream, and simply returns the next parsed
Genbank Stone, or undef if there is nothing more to fetch. It has the same semantics
as the parent class, including the ability to restrict access to certain top-level
tags.
The object returned is a Stone::GB_Sequence object, which is a descendent of Stone.
put()
The put() method is inherited from the parent Boulder::Stream class, and will write
the passed Stone to standard output in Boulder format. This means that it is
currently not possible to write a Boulder::Genbank object back into Genbank flatfile
form.
Extended Entrez Parameters
The Entrez accessor recognizes extended parameters that allow you the ability to customize
the search. Instead of passing a query string scalar or a list of accession numbers as
the -fetch argument, pass a hash reference. The hashref should contain one or more of the
following keys:
-query
The Entrez query to process.
-accession
The list of accession numbers to fetch, as an array ref.
-db The database to search. This is a single-letter database code selected from the
following list:
m MEDLINE
p Protein
n Nucleotide
s Popset
-proxy
An HTTP proxy to use. For example:
-proxy => http://www.firewall.com:9000
If you think you need this, get the correct URL from your system administrator.
As an example, here's how to search for ESTs from Oryza sativa that have been entered or
modified since 1999.
my $gb = new Boulder::Genbank( -accessor=>Entrez,
-query=>'Oryza sativa[Organism] AND EST[Keyword] AND 1999[MDAT]',
-db => 'n'
});
METHODS DEFINED BY THE GENBANK STONE OBJECT
Each record returned from the Boulder::Genbank stream defines a set of methods that
correspond to features and other fields in the Genbank flat file record.
Stone::GB_Sequence gives the full details, but they are listed for reference here:
$length = $entry->length
Get the length of the sequence.
$start = $entry->start
Get the start position of the sequence, currently always "1".
$end = $entry->end
Get the end position of the sequence, currently always the same as the length.
@feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon'])
features() will search the entry feature list for those features that meet certain
criteria. The criteria are specified using the -pos and/or -type argument names, as shown
below.
-pos
Provide a position or range of positions which the feature must overlap. A single
position is specified in this way:
-pos => 1500; # feature must overlap postion 1500
or a range of positions in this way:
-pos => [1000,1500]; # 1000 to 1500 inclusive
If no criteria are provided, then features() returns all the features, and is
equivalent to calling the Features() accessor.
-type, -types
Filter the list of features by type or a set of types. Matches are case-insensitive,
so "exon", "Exon" and "EXON" are all equivalent. You may call with a single type as
in:
-type => 'Exon'
or with a list of types, as in
-types => ['Exon','CDS']
The names "-type" and "-types" can be used interchangeably.
$seqObj = $entry->bioSeq;
Returns a Bio::Seq object from the Bioperl project. Dies with an error message unless the
Bio::Seq module is installed.
OUTPUT TAGS
The tags returned by the parsing operation are taken from the NCBI ASN.1 schema. For
consistency, they are normalized so that the initial letter is capitalized, and all
subsequent letters are lowercase. This section contains an abbreviated list of the most
useful/common tags. See "The NCBI Data Model", by James Ostell and Jonathan Kans in
"Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" (Eds. A.
Baxevanis and F. Ouellette), pp 121-144 for the full listing.
Top-Level Tags
These are tags that appear at the top level of the parsed Genbank entry.
Accession
The accession number of this entry. Because of the vagaries of the Genbank data
model, an entry may have multiple accession numbers (e.g. after a merging operation).
Accession may therefore be a multi-valued tag.
Example:
my $accessionNo = $s->Accession;
Authors
The list of authors, as they appear on the AUTHORS line of the Genbank record. No
attempt is made to parse them into individual authors.
Basecount
The nucleotide basecount for the entry. It is presented as a Boulder Stone with keys
"a", "c", "t" and "g". Example:
my $A = $s->Basecount->A;
my $C = $s->Basecount->C;
my $G = $s->Basecount->G;
my $T = $s->Basecount->T;
print "GC content is ",($G+$C)/($A+$C+$G+$T),"\n";
Blob
The entire flatfile record as an unparsed chunk of text (a "blob"). This is a handy
way of reassembling the record for human inspection.
Comment
The COMMENT line from the Genbank record.
Definition
The DEFINITION line from the Genbank record, unmodified.
Features
The FEATURES table. This is a complex stone object with multiple subtags. See the
"The Features Tag" for details.
Journal
The JOURNAL line from the Genbank record, unmodified.
Keywords
The KEYWORDS line from the Genbank record, unmodified. No attempt is made to parse
the keywords into separate values.
Example:
my $keywords = $s->Keywords
Locus
The LOCUS line from the Genbank record. It is not further parsed.
Medline, Nid
References to other database accession numbers.
Organism
The taxonomic name of the organism from which this entry was derived. This line is
taken from the Genbank entry unmodified. See the NCBI data model documentation for an
explanation of their taxonomic syntax.
Reference
The REFERENCE line from the Genbank entry. There are often multiple Reference lines.
Example:
my @references = $s->Reference;
Sequence
The DNA or RNA sequence of the entry. This is presented as a single lower-case
string, with all base numbers and formatting characters removed.
Source
The entry's SOURCE field; often giving clues on how the sequencing was performed.
Title
The TITLE field from the paper describing this entry, if any.
The Features Tag
The Features tag points to a Stone record that contains multiple subtags. Each subtag is
the name of a feature which points, in turn, to a Stone that describes the feature's
location and other attributes. The full list of feature is beyond this document, but the
following are the features that are most often seen:
Cds a CDS
Intron an intron
Exon an exon
Gene a gene
Mrna an mRNA
Polya_site a putative polyadenylation signal
Repeat_unit a repetitive region
Source More information about the organism and cell
type the sequence was derived from
Satellite a microsatellite (dinucleotide repeat)
Each feature will contain one or more of the following subtags:
DB_xref
A cross-reference to another database in the form DB_NAME:accession_number. See the
NCBI Web site for a description of these cross references.
Evidence
The evidence for this feature, either "experimental" or "predicted".
Gene
If the feature involves a gene, this will be the gene's name (or one of its names).
This subtag is often seen in "Gene" and Cds features.
Example:
foreach ($s->Features->Cds) {
my $gene = $_->Gene;
my $position = $_->Position;
Print "Gene $gene ($position)\n";
}
Map If the feature is mapped, this provides a map position, usually as a cytogenetic band.
Note
A grab-back for various text notes.
Number
When multiple features of this type occur, this field is used to number them.
Ordinarily this field is not needed because Boulder::Genbank preserves the order of
features.
Organism
If the feature is Source, this provides the source organism.
Position
The position of this feature, usually expresed as a range (1970..1975).
Product
The protein product of the feature, if applicable, as a text string.
Translation
The protein translation of the feature, if applicable.
SEE ALSO
Boulder, Boulder::Blast
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 1997-2000 Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same
terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
EXAMPLE GENBANK OBJECT
The following is an excerpt from a moderately complex Genbank Stone. The Sequence line
and several other long lines have been truncated for readability.
Authors=Spritz,R.A., Strunk,K., Surowy,C.S.O., Hoch,S., Barton,D.E. and Francke,U.
Authors=Spritz,R.A., Strunk,K., Surowy,C.S. and Mohrenweiser,H.W.
Locus=HUMRNP7011 2155 bp DNA PRI 03-JUL-1991
Accession=M57939
Accession=J04772
Accession=M57733
Keywords=ribonucleoprotein antigen.
Sequence=aagcttttccaggcagtgcgagatagaggagcgcttgagaaggcaggttttgcagcagacggcagtgacagcccag...
Definition=Human small nuclear ribonucleoprotein (U1-70K) gene, exon 10 and 11.
Journal=Nucleic Acids Res. 15, 10373-10391 (1987)
Journal=Genomics 8, 371-379 (1990)
Nid=g337441
Medline=88096573
Medline=91065657
Features={
Polya_site={
Evidence=experimental
Position=1989
Gene=U1-70K
}
Polya_site={
Position=1990
Gene=U1-70K
}
Polya_site={
Evidence=experimental
Position=1992
Gene=U1-70K
}
Polya_site={
Evidence=experimental
Position=1998
Gene=U1-70K
}
Source={
Organism=Homo sapiens
Db_xref=taxon:9606
Position=1..2155
Map=19q13.3
}
Cds={
Codon_start=1
Product=ribonucleoprotein antigen
Db_xref=PID:g337445
Position=join(M57929:329..475,M57930:183..245,M57930:358..412, ...
Gene=U1-70K
Translation=MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTR...
}
Cds={
Codon_start=1
Product=ribonucleoprotein antigen
Db_xref=PID:g337444
Evidence=experimental
Position=join(M57929:329..475,M57930:183..245,M57930:358..412, ...
Gene=U1-70K
Translation=MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPR...
}
Polya_signal={
Position=1970..1975
Note=putative
Gene=U1-70K
}
Intron={
Evidence=experimental
Position=1100..1208
Gene=U1-70K
}
Intron={
Number=10
Evidence=experimental
Position=1100..1181
Gene=U1-70K
}
Intron={
Number=9
Evidence=experimental
Position=order(M57937:702..921,1..1011)
Note=2.1 kb gap
Gene=U1-70K
}
Intron={
Position=order(M57935:272..406,M57936:1..284,M57937:1..599, <1..>1208)
Gene=U1-70K
}
Intron={
Evidence=experimental
Position=order(M57935:284..406,M57936:1..284,M57937:1..599, <1..>1208)
Note=first gap-0.14 kb, second gap-0.62 kb
Gene=U1-70K
}
Intron={
Number=8
Evidence=experimental
Position=order(M57935:272..406,M57936:1..284,M57937:1..599, <1..>1181)
Note=first gap-0.14 kb, second gap-0.62 kb
Gene=U1-70K
}
Exon={
Number=10
Evidence=experimental
Position=1012..1099
Gene=U1-70K
}
Exon={
Number=11
Evidence=experimental
Position=1182..(1989.1998)
Gene=U1-70K
}
Exon={
Evidence=experimental
Position=1209..(1989.1998)
Gene=U1-70K
}
Mrna={
Product=ribonucleoprotein antigen
Position=join(M57928:358..668,M57929:319..475,M57930:183..245, ...
Gene=U1-70K
}
Mrna={
Product=ribonucleoprotein antigen
Citation=[2]
Evidence=experimental
Position=join(M57928:358..668,M57929:319..475,M57930:183..245, ...
Gene=U1-70K
}
Gene={
Position=join(M57928:207..719,M57929:1..562,M57930:1..577, ...
Gene=U1-70K
}
}
Reference=1 (sites)
Reference=2 (bases 1 to 2155)
=