What's New in Sockeye 1.3
Improved User Assistance
From Sockeye: "Ask Us questions Dialog" and get immediate help via MSN Messenger. Click here for more details
Handling Gene List
Users can import a whole list of genes at once in Sockeye using Retrieval Wizard
Eponine annotations are added to detect mammalian transcription start sites.
MCS pipeline is added to detect MCSs, or Multi-species Conserved Sequences, from multiple sequence tracks in Sockeye
Details of MCS can be found here
New Algorithms For Alignment and Motif Discovery
Alignment program CONREAL has been added
Motif discovery algorithm (w)consensus and MEME have also been added
New Sanners Available
Sockeye can now read and scan Motifsampler output files and site sequences files
Feature Score Normalization
This new feature allows users to compare different types of scored features on same or different tracks visually
Set Operation Dialog
"Virtual regions" answer questions like "show me all features that fall withing the upstream region (or vincinity) of e.g. my genes"
Support current and all historical Ensembl releases
Minor Bugs and Issues Fixed
Sockeye for Linux uses Java 1.4.1 and Java3D 1.3.1 beta 1.
Sockeye for Windows uses Java 1.4.2 and Java3D 1.3.1.