Difference between revisions of "GBrowse Adaptors"
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| Bio::DB::GFF | | 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 | ||
| Doesn't always work well with some GFF3 formated data | | Doesn't always work well with some GFF3 formated data | ||
|- | |- | ||
| Bio::DB::SeqFeature::Store | | Bio::DB::SeqFeature::Store | ||
| − | | MySQL | + | | [[MySQL]] |
| Relatively few (due to it's being relatively new) | | 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 | | Roughly 4X faster than Bio::DB::GFF for the same data; designed to work will GFF3 | ||
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| Bio::DB::Das::Chado | | 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 | ||
| Allows 'live' viewing of the features in a Chado database | | Allows 'live' viewing of the features in a Chado database | ||
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| Bio::DB::Das::BioSQL | | 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 | ||
| Allows 'live' viewing of the features in a BioSQL database | | Allows 'live' viewing of the features in a BioSQL database | ||
Revision as of 19:03, 23 January 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 |
