This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
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 (use bp_seqfeature_load.pl)||MySQL, PostgreSQL, SQLite, BerkeleyDB||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 (use bp_load_gff.pl, bp_bulk_load_gff.pl, bp_fast_load_gff.pl)||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::Sam (available from CPAN)||SAMtools||Growing (particularly with GBrowse2)||Very fast access to NextGen sequencing data||Difficult to use with GBrowse 1.70|
|Bio::DB::BigWig and Bio::DB::BigWigSet (available from CPAN)||UCSC Formats||Growing (particularly with GBrowse2)||Very fast access to data in bigWig format||Difficult to use with GBrowse 1.70|
|Bio::DB::BigBed (available from CPAN)||UCSC Formats||Growing (particularly with GBrowse2)||Very fast access to data in bigBed format||Difficult to use with GBrowse 1.70|
|Bio::DB::Das::Chado (available from CPAN)||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 (available from CPAN)||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 using either Bio::DB::GFF or SeqFeature::Store)||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|
There have been some useful email threads on adaptor choices and tradeoffs.
- Memory Database, 2010/06