The guides below walkthrough the annotation of the Snail gene in Strongylocentrotus purpuratus (purple sea urchin).

Annotator's Instructions.pdf
Annotator's FAQ.pdf

CYRENE Publications and Presentations

• Sorin Istrail, Ryan Tarpine, Kyle Schutter, Derek Aguiar, "Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks", Chapter in Computational Biology of Transcription Factor Binding, Humana Press, vol. 674, pp. 369-399, 2010.
• Poster presented at the Developmental Biology of the Sea Urchin Meeting in 2011

CYRENE offers robust annotation capabilities.

The cis-Browser and cis-Lexicon are the two core components of the CYRENE project. The cis-Lexicon is a database for all types of cis-regulatory information, with an emphasis on site and module function and logic. The browser is partly a view of the cis-Lexicon, but more fully it is designed as a laboratory for the researcher to use throughout his experiments.

The figures and graphs used in published papers display volumes of information in a small space, and help to communicate many of the researcher's insights into the problem he is studying. As he is performing his experiments, however, this type of view is unavailable. A powerful, visual environment for integrating known genomic information and experimental data would allow him to better formulate new hypotheses for testing in the lab. The cis-Browser is built upon the the Celera Genome Browser, an application developed by a team of programmers over several years with constant input from biologists and ultimately released as Open Source software. The cis-Browser itself is released under the LGPL license, permitting non-commercial modification and use of its source code.