What's New in Sockeye 1.3
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Improved User Assistance
From Sockeye: "Ask Us questions Dialog" and get immediate help via MSN Messenger. Click here for more details
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Handling Gene List
Users can import a whole list of genes at once in Sockeye using Retrieval Wizard
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Eponine Annotations
Eponine annotations are added to detect mammalian transcription start sites.
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MCS Analysis
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
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New Algorithms For Alignment and Motif Discovery
Alignment program CONREAL has been added
Motif discovery algorithm (w)consensus and MEME have also been added
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New Sanners Available
Sockeye can now read and scan Motifsampler output files and site sequences files
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Feature Score Normalization
This new feature allows users to compare different types of scored features on same or different tracks visually
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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"
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Support current and all historical Ensembl releases
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Minor Bugs and Issues Fixed
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Java
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.