About Sockeye

Sockeye is a Java application designed to assemble, view and work with genomic information in a 3D environment. Sockeye has been developed with a focus on displaying potential gene regulatory regions and for running and visualising the results from regulatory element detection approaches and algorithms.This program links to the Ensembl database and displays genomic features along tracks (stretches of DNA). It is very flexible with genomic data in GFF files. This application allows users to seamlessly visualize large amount of information at disparate locations in the genome. The application allows user to use varaity of algoritms for (mulitple) sequence alignment and displays comprehencive results of alignment.

Sockeye will be an open source project. It represents the ongoing efforts of many dedicated individuals to create a genome viewer that gives users the facility to analyze features from the very big (karyotypes) to the very small (snps and transcription factor binding sites).

Sockeye research and development has been funded by Genome Canada. It is the core data viewer of the Bioinformatics of Mammalian Gene Expression project. For more information, please feel free to ask us questions on our Sockeye mailing list.

Source code will be freely available from the authors for non-commercial use, please contact Asim Siddiqui (


Sockeye v1.2 is available as of Friday, 21 May, 2004, from the Download page. Java WebStart version

This version offers improved functionality for comparative genomics, an improved GUI, and 'on-demand annotations' to permit querying large genomic regions. To check out the newest features in Sockeye, please click What's New in Sockeye page.


Sockeye supports a constantly increasing number of algorithms like alignments, motif discovery or motif scans. To view the latest algorithms in Sockeye, please view Algorithms page

See Sockeye in Action

To explore all the features Sockeye provides and see how easy it will be to run Sockeye on your computer, please select:


Sockeye video tutorials


Sockeye screenshots

Page last modified Feb 06, 2007