GBrowse Adaptors
From GMOD
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 (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 |