A gem to use the Distributed Annotation System with Ruby.

DAS

The Distributed Annotation System is a protocol developed to allow the distributed annotation of nucleotide and protein sequences. DAS servers are used to deliver reference sequences and/or annotations for those sequences. DAS clients can be used to remix the information from different sources and deliver a single representation of the information. Examples for DAS-clients are ENSEMBL Genome Browser, Spice and Dalliance.

Widely-used DAS-server-implementations are myDAS – which is based on Java – and ProServer which is based on Perl.

RubyDAS

RubyDAS tries to provide a reference- and annotation-server with the DAS 1.6 standard based on Ruby. Reference-sequences and the annotations are stored in a database of choice using Datamapper. The dependencies of RubyDAS as of now are:

• BioRuby
• Sinatra
• http://datamapper.org/

Features

• Read GFF3
• Read FASTA
• DAS sequences-command
• DAS sources-command
• DAS features-commands

How-To

To test the current implementation just run server.rb and point your browser to localhost:4567/das/rubydas/sequence?segment=MAL5:1000,2000 localhost:4567/das/rubydas/types?segment=MAL5:1000,2000 or localhost:4567/das/rubydas/features?segment=MAL5:1000,2000

To-Do

• Implement entry_points
• Implement sources
• Add further input-file-formats
• Test compatibility with DAS-clients

Contact

If you are interested in joining the development of RubyDAS you can join the Google Group/mailinglist at https://groups.google.com/group/rubydas