Difference between revisions of "GBrowse Adaptors"

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! Cons
 
! Cons
 
|-
 
|-
| Bio::DB::GFF
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| {{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]])
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| Doesn't always work well with some GFF3 formated data
 
| Doesn't always work well with some GFF3 formated data
 
|-
 
|-
| Bio::DB::SeqFeature::Store
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| {{BPM|Bio::DB::SeqFeature::Store}}
 
| [[MySQL]]
 
| [[MySQL]]
 
| Relatively few (due to it's being relatively new)
 
| Relatively few (due to it's being relatively new)
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| 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
 
| 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
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| {{BPM|Bio::DB::Das::Chado}}
 
| [[PostgreSQL]] and a [[Chado]] [[Glossary#Database Schema|schema]]
 
| [[PostgreSQL]] and a [[Chado]] [[Glossary#Database Schema|schema]]
 
| Relatively few due to the specialized nature of Chado
 
| Relatively few due to the specialized nature of Chado
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| Slow compared to Bio::DB::GFF
 
| Slow compared to Bio::DB::GFF
 
|-
 
|-
| Bio::DB::Das::BioSQL
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| {{BPM|Bio::DB::Das::BioSQL}}
 
| [[MySQL]] and a [[BioSQL]] schema
 
| [[MySQL]] and a [[BioSQL]] schema
 
| Relatively few due to the small number of BioSQL users
 
| Relatively few due to the small number of BioSQL users
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| Lucene (searches indexed flat files)
 
| Lucene (searches indexed flat files)
 
| Relatively few
 
| Relatively few
|  
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|
|  
+
|
 
|}
 
|}
 
  
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]
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[[Category:DAS]]

Revision as of 21:32, 1 February 2008

GBrowse has available several adaptors (yes, it is spelled that way and is not "adapters") available for several different data sources. A common question is "which adaptor should I be using?" This page is an attempt to answer that question.


Adaptor Other required software Roughly how many users Pros Cons
Bio::DB::GFF A relational database server: MySQL, PostgreSQL, Oracle, or BerkeleyDB Lots! (Especially MySQL) Quite fast; large user base Doesn't always work well with some GFF3 formated data
Bio::DB::SeqFeature::Store MySQL Relatively few (due to it's being relatively new) 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 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 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