Difference between revisions of "GBrowse Adaptors"

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(Flagged GFF2 as deprecated.)
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! Pros
 
! Pros
 
! Cons
 
! Cons
 +
|-
 +
| {{BPM|Bio::DB::SeqFeature::Store}}
 +
| [[MySQL]]
 +
| Many and growing fast.
 +
| Roughly 4X faster than Bio::DB::GFF for the same data; designed to work with [[GFF3]]
 +
| Developed for use with [[GFF3]]; about 2X slower than Bio::DB::GFF to load a database
 
|-
 
|-
 
| {{BPM|Bio::DB::GFF}}
 
| {{BPM|Bio::DB::GFF}}
 
| A [[Glossary#Database Management System|relational database server]]: [[MySQL]], [[PostgreSQL]], Oracle, or BerkeleyDB
 
| A [[Glossary#Database Management System|relational database server]]: [[MySQL]], [[PostgreSQL]], Oracle, or BerkeleyDB
 
| Lots! (Especially [[MySQL]])
 
| Lots! (Especially [[MySQL]])
| Quite fast; large user base
+
| Quite fast; large user base; Have to use this if your data is in the (now deprecated) [[GFF2]] format.
| Doesn't always work well with some GFF3 formated data
+
| Does not work well with [[GFF3]] formatted data
|-
+
| {{BPM|Bio::DB::SeqFeature::Store}}
+
| [[MySQL]]
+
| Relatively few (due to it's being relatively new), but growing fast
+
| Roughly 4X faster than Bio::DB::GFF for the same data; designed to work will GFF3
+
| Still a new tool developed for use with GFF3 so there is a much smaller user base; about 2X slower than Bio::DB::GFF to load a database
+
 
|-
 
|-
 
| Bio::DB::Das::Chado (distributed with [[GBrowse]])
 
| Bio::DB::Das::Chado (distributed with [[GBrowse]])

Revision as of 21:24, 30 December 2008

GBrowse has a flexible adaptor (yes, it is spelled that way and is not "adapter") system for running off various types of databases/sources. A common question is "which adaptor should I be using?" This attempts to answer that question.

Adaptor Other required software Roughly how many users Pros Cons
Bio::DB::SeqFeature::Store MySQL Many and growing fast. Roughly 4X faster than Bio::DB::GFF for the same data; designed to work with GFF3 Developed for use with GFF3; about 2X slower than Bio::DB::GFF to load a database
Bio::DB::GFF A relational database server: MySQL, PostgreSQL, Oracle, or BerkeleyDB Lots! (Especially MySQL) Quite fast; large user base; Have to use this if your data is in the (now deprecated) GFF2 format. Does not work well with GFF3 formatted data
Bio::DB::Das::Chado (distributed with GBrowse) PostgreSQL and a Chado schema Relatively few due to the specialized nature of Chado Allows 'live' viewing of the features in a Chado database Slow compared to Bio::DB::GFF
Bio::DB::Das::BioSQL (distributed with GBrowse) MySQL and a BioSQL schema Relatively few due to the small number of BioSQL users Allows 'live' viewing of the features in a BioSQL database Slow compared to Bio::DB::GFF
Memory (ie, flat file database) None For real servers, none Easy for rapid development and testing Very slow for more than a few thousand features
LuceGene Lucene (searches indexed flat files) Relatively few