A user now has 3D move/zoom controls that are comparable to those in 2D genomic browsers for work with individual data tracks, but have been extended to support multi-track comparative genomics / algorithmics work. Key extensions include regions, multiple-selection operations and behaviours for coexisting tracks.
As a first stage in implementing several ways of assembling collections of related genes, all Ensembl homologues for a gene can easily be assembled in 3D, using a popup menu from the gene.
Pairs and multiple sequences can be aligned from Sockeye. Different algorithms can be used. Typically you would define the sequences by marking, then selecting, a region on each of set of data tracks that show a collection of related genes.
Sockeye is now using Java 1.4.1_01 and Java3D 1.3.1 beta 1.
user_config.xml
. When this is
set to true for a feature type, a feature instance that
overlaps another of that type will be separated in 3D. Currently, Java3D has an
undocumented limited ability to handle multibody overlaps, and this constrains
the performance of this functionality in Sockeye.kaka.sanger.ac.uk
and
from bcgsc.bc.ca
, www.ensembl.org/java/download/
states
(as of 07aug03) that the 26 Jun 2003
Ensembl Java 'layer'
used by Sockeye to access Ensembl servers supports v14, but only partially
supports v15, 13, 12 and 11.user_config.xml
is now checked as it is loaded during startup.
Format errors are reported in detail, though without line numbers. <featuresLimit>
features.cone.WRL
: 3 for
upside down, 2 for upright. These are not yet in use for Ensembl features. featuresLimit
. Added featuresLimit
below feature tree.user_config.XML
file and temporarily in the Options panel.Last modified: 14 August 2003, 12h15