Difference between revisions of "GBrowse Adaptors"
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! Pros | ! Pros | ||
! Cons | ! Cons | ||
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+ | | {{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 | ||
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| {{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. |
− | | | + | | Does not work well with [[GFF3]] formatted data |
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| 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 |
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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 |