DBI interface

SeqCrawler provides a DBI interface as a Perl module to link GBrowse2 with the Solr index.

A simple configuration in gbrowse specific configuration file is needed to do so:

  db_args       = -adaptor    solr
    -STORAGEURL http://my_riak_external_hostname:riak_port/riak
    -BANK       GenBank (optional, default is all)


Available options are the following

db_args       = -adaptor    solr
                                // Following is optional
                -port (default: 8080, solr server port)
                -host  (default: localhost, solr server host)
                -maxresult (default: 99999999, max mnuber of returned results)
                -BANK (default: all, bank name in index as a filter)
                -STORAGEURL (default: undefined, url to the sequence backend. If not set, dna or protein sequences will not be retrieved)

Features configuration

The system is preconfigured for a number of features (rna, cds, ...). However, if indexed data adds new features, the gbrowse configuration should be updated to specify their display. To do so, edit the seqcrawler configuration file (/etc/gbrowse2/gbrowse.conf/seqcrawler.conf) and append the new features (see GBrowse configuration manual). Example:

feature  = chromosome
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = chromosome
citation = chromosome
category = Analysis
das category = experimental

Web interface

GBrowse provides a web interface to visualize a genome and browse it. It is interfaced to the index to get GFF features for a chromosome with positions etc... The user can click on a gene to gets its details, or change the select area. There are also some export functions available.

The interface and behavior is customizable help with a very functional configuration file. For more information, refer to the GBrowse tutorial.

GBrowse2 screen