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Main.HomePage History
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August 07, 2008, at 06:35 AM
by 131.111.60.110 -
Changed line 9 from:
* fast querying of overlap, contains and contained-in queries ("range queries") to:
* fast querying of overlap, contains and contained-in queries August 07, 2008, at 06:32 AM
by 131.111.60.110 -
Changed lines 3-4 from:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make fast overlap, contains and contained-in queries.
to:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to improve the speed of overlap, contains and contained-in queries
August 07, 2008, at 06:30 AM
by 131.111.60.110 -
Changed line 8 from:
* adds a PostgreSQL range type to:
* adds a PostgreSQL integer range type August 07, 2008, at 06:25 AM
by 131.111.60.110 -
Changed lines 3-4 from:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make overlap, contains and contained-in queries fast.
to:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make fast overlap, contains and contained-in queries.
October 17, 2007, at 08:28 AM
by 131.111.60.110 -
Changed line 9 from:
* fast querying of overlap, contains and contained-in queries to:
* fast querying of overlap, contains and contained-in queries ("range queries") October 17, 2007, at 08:26 AM
by 131.111.60.110 -
Changed lines 11-12 from:
* tested with PostgreSQL 8.2 and 8.3
to:
Added lines 14-15:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] has been tested with PostgreSQL 8.2 and 8.3
October 17, 2007, at 08:25 AM
by 131.111.60.110 -
Changed lines 11-12 from:
to:
* tested with PostgreSQL 8.2 and 8.3
August 19, 2007, at 05:30 AM
by 82.69.238.134 -
Changed line 8 from:
to:
* adds a PostgreSQL range type August 18, 2007, at 10:29 AM
by 131.111.60.110 -
Deleted lines 6-7:
[[http://bioinformatics.org/project/?group_id=793 | Project page]] at [[http://bioinformatics.org | Bioinformatics.org]]
August 17, 2007, at 01:33 PM
by 131.111.60.110 -
Changed line 18 from:
Release are listed in the [[http://bioinformatics.org/project/filelist.php?group_id=793 | files section]] to:
Releases are listed in the [[http://bioinformatics.org/project/filelist.php?group_id=793 | files section]] August 17, 2007, at 12:35 PM
by 131.111.60.110 -
Changed line 21 from:
The development code is avaiable in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command: to:
The development code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command: August 17, 2007, at 12:35 PM
by 131.111.60.110 -
Changed lines 16-18 from:
!!! Code
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command: to:
!!! Downloads
Release are listed in the [[http://bioinformatics.org/project/filelist.php?group_id=793 | files section]]
of the project pages.
The development code is avaiable in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command: August 17, 2007, at 12:05 PM
by 131.111.60.110 -
Changed lines 14-16 from:
!!!Query Example
Find all features overlapping the base range 2000..3000: to:
See the [[BiosegUsage | bioseg usage]] page for examples.
!!! Code
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command: Changed lines 20-21 from:
select * from feature
where bioseg_create(2000, 3000) && bioseg_create(fmin, fmax); to:
svn checkout svn://bioinformatics.org/svnroot/bioseg/trunk bioseg Changed lines 22-60 from:
or:
[@
select * from feature
where '2000..3000'::bioseg && bioseg_create(fmin, fmax);
@]
The "&&" is the overlaps operator, the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg | README]] for a full list of operators.
!!!Index Creation
The speed of the query above will be improved by creating a function index:
[@
create index test on feature using gist (bioseg_create(fmin, fmax));
@]
!!!Using the bioseg type directly
The bioseg type can be used as a column type. eg.
[@
CREATE TABLE test_bioseg (id integer, name text, seg bioseg);
@]
and populated like this:
[@
insert into test_bioseg values (1, 'some_name', '1000..2000'::bioseg);
@]
then queried:
[@
select * from test_bioseg where seg && '200..3000'::bioseg;
@]
There are more example queries in [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2Fsql%2Fbioseg.sql | sql/bioseg.sql]].
!!! Code
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command:
[@
svn checkout svn://bioinformatics.org/svnroot/bioseg/trunk bioseg
@]
to:
August 17, 2007, at 12:02 PM
by 131.111.60.110 -
Deleted lines 4-8:
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command:
[@
svn checkout svn://bioinformatics.org/svnroot/bioseg/trunk bioseg
@]
Changed lines 52-59 from:
to:
!!! Code
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command:
[@
svn checkout svn://bioinformatics.org/svnroot/bioseg/trunk bioseg
@]
August 17, 2007, at 10:47 AM
by 131.111.60.110 -
Changed lines 3-4 from:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL[[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make overlap, contains and contained-in queries fast.
to:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make overlap, contains and contained-in queries fast.
August 17, 2007, at 10:46 AM
by 131.111.60.110 -
Changed lines 3-4 from:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for PostgreSQL. A [[http://www.postgresql.org | PostgreSQL]] [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make overlap, contains and contained-in queries fast.
to:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for [[http://www.postgresql.org | PostgreSQL]]. A PostgreSQL[[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make overlap, contains and contained-in queries fast.
Changed line 15 from:
* adds a real PostgreSQL type to:
August 17, 2007, at 10:45 AM
by 131.111.60.110 -
Changed lines 1-4 from:
!!Introduction
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for PostgreSQL. A PostgreSQL GiST index is used to make overlap, contains and contained-in queries fast.
to:
!!!Introduction
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for PostgreSQL. A [[http://www.postgresql.org | PostgreSQL]] [[http://www.postgresql.org/docs/8.1/static/gist.html | GiST]] index is used to make overlap, contains and contained-in queries fast.
Added lines 14-18:
!!! Features
* adds a real PostgreSQL type
* fast querying of overlap, contains and contained-in queries
* inter-base or 1-based coordinate system
August 15, 2007, at 12:19 PM
by 131.111.60.110 -
Changed lines 52-54 from:
(:html:)<script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> to:
(:html:)
<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
August 15, 2007, at 12:19 PM
by 131.111.60.110 -
Added lines 51-58:
(:html:)<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
</script>
<script type="text/javascript">
_uacct = "UA-2423978-1";
urchinTracker();
</script>
(:htmlend:)
August 15, 2007, at 09:27 AM
by 131.111.60.110 -
Changed line 16 from:
Find all features overlapping the base range 20000..30000: to:
Find all features overlapping the base range 2000..3000: Changed line 19 from:
where bioseg_create(20000, 30000) && bioseg_create(fmin, fmax); to:
where bioseg_create(2000, 3000) && bioseg_create(fmin, fmax); Changed line 24 from:
where '20000..30000'::bioseg && bioseg_create(fmin, fmax); to:
where '2000..3000'::bioseg && bioseg_create(fmin, fmax); Changed line 43 from:
insert into test_bioseg values (100, 'some_name', '1000..2000'::bioseg); to:
insert into test_bioseg values (1, 'some_name', '1000..2000'::bioseg); Changed line 47 from:
select * from test_bioseg where seg && '200..30000'::bioseg; to:
select * from test_bioseg where seg && '200..3000'::bioseg; August 15, 2007, at 09:26 AM
by 131.111.60.110 -
Changed lines 23-24 from:
select * from feature where '20000..30000'::bioseg && bioseg_create(fmin, fmax); to:
select * from feature
where '20000..30000'::bioseg && bioseg_create(fmin, fmax); August 15, 2007, at 09:25 AM
by 131.111.60.110 -
Changed lines 18-19 from:
select * from feature where bioseg_create(20000, 30000) && bioseg_create(fmin, fmax); to:
select * from feature
where bioseg_create(20000, 30000) && bioseg_create(fmin, fmax); August 15, 2007, at 09:14 AM
by 131.111.60.110 -
Changed line 5 from:
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F&sc=0 | subversion repository]] at Bioinformatics.org. It can be checked out with this command: to:
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F | subversion repository]] at Bioinformatics.org. It can be checked out with this command: Changed lines 10-11 from:
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]].
to:
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg | README]].
Changed lines 24-25 from:
The "&&" is the overlaps operator, the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]] for a full list of operators.
to:
The "&&" is the overlaps operator, the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg | README]] for a full list of operators.
August 15, 2007, at 09:13 AM
by 131.111.60.110 -
Added lines 47-48:
There are more example queries in [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2Fsql%2Fbioseg.sql | sql/bioseg.sql]].
August 15, 2007, at 08:20 AM
by 131.111.60.110 -
Changed lines 14-15 from:
to:
Changed line 22 from:
select * from feature where "20000..30000"::bioseg && bioseg_create(fmin, fmax); to:
select * from feature where '20000..30000'::bioseg && bioseg_create(fmin, fmax); Changed lines 24-26 from:
to:
The "&&" is the overlaps operator, the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]] for a full list of operators.
!!!Index Creation
Changed lines 31-46 from:
to:
@]
!!!Using the bioseg type directly
The bioseg type can be used as a column type. eg.
[@
CREATE TABLE test_bioseg (id integer, name text, seg bioseg);
@]
and populated like this:
[@
insert into test_bioseg values (100, 'some_name', '1000..2000'::bioseg);
@]
then queried:
[@
select * from test_bioseg where seg && '200..30000'::bioseg;
@] August 15, 2007, at 08:11 AM
by 131.111.60.110 -
Added lines 1-2:
Changed lines 12-30 from:
[[http://bioinformatics.org/project/?group_id=793 | Project page]] at [[http://bioinformatics.org | Bioinformatics.org]] to:
[[http://bioinformatics.org/project/?group_id=793 | Project page]] at [[http://bioinformatics.org | Bioinformatics.org]]
!!Query Example
Find all features overlapping the base range 20000..30000:
[@
select * from feature where bioseg_create(20000, 30000) && bioseg_create(fmin, fmax);
@]
or:
[@
select * from feature where "20000..30000"::bioseg && bioseg_create(fmin, fmax);
@]
!!Index Creation
The speed of the query above will be improved by creating a function index:
[@
create index test on feature using gist (bioseg_create(fmin, fmax));
@] August 15, 2007, at 05:39 AM
by 131.111.60.110 -
Changed lines 1-3 from:
BIOSEG is an implementation of a biological sequence interval type for PostgreSQL. A PostgreSQL GiST index is used to make overlap, contains and contained-in queries fast. The code is based on the SEG datatype supplied with PostgreSQL.
The code is checked into a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F&sc=0 | Subversion repository]] at Bioinformatics.org. It can be checked out with this command: to:
[[http://bioinformatics.org/project/?group_id=793 | BIOSEG]] is an implementation of a biological sequence interval/range type for PostgreSQL. A PostgreSQL GiST index is used to make overlap, contains and contained-in queries fast.
The code is available in a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F&sc=0 | subversion repository]] at Bioinformatics.org. It can be checked out with this command: Changed lines 8-9 from:
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]]
to:
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]].
August 14, 2007, at 07:50 PM
by 82.69.238.134 -
Changed line 3 from:
The code is checked into a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F&sc=0 | Subversion repository]] at bioinformatics.org. It can be checked out with this command: to:
The code is checked into a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F&sc=0 | Subversion repository]] at Bioinformatics.org. It can be checked out with this command: Changed lines 8-10 from:
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]] to:
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]]
[[http://bioinformatics.org/project/?group_id=793 | Project page]] at [[http://bioinformatics.org | Bioinformatics.org]] August 14, 2007, at 07:47 PM
by 82.69.238.134 -
Changed lines 6-8 from:
to:
@]
Installation instructions and documentation are in the [[http://bioinformatics.org/websvn/filedetails.php?repname=bioseg&path=%2Ftrunk%2FREADME.bioseg&rev=0&sc=0 | README]] August 14, 2007, at 07:44 PM
by 82.69.238.134 -
Added lines 1-6:
BIOSEG is an implementation of a biological sequence interval type for PostgreSQL. A PostgreSQL GiST index is used to make overlap, contains and contained-in queries fast. The code is based on the SEG datatype supplied with PostgreSQL.
The code is checked into a [[http://bioinformatics.org/websvn/listing.php?repname=bioseg&path=%2F&sc=0 | Subversion repository]] at bioinformatics.org. It can be checked out with this command:
[@
svn checkout svn://bioinformatics.org/svnroot/bioseg/trunk bioseg
@]
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