GBrowse Adaptors

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 or PostgreSQL	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