Team sequoia

Overall Objectives
Scientific Foundations
New Results
Contracts and Grants with Industry
Other Grants and Activities

Section: Software

CG-seq – comparative genomics

Genome annotation by comparative genomics is a common motivating background of several research subjects in the team: sequence processing, noncoding RNAs,...In this perspective, we have developed the CG-seq package, that gathers several tools for this task. The purpose of CG-seq is to identify functional regions in a genomic sequence by comparative analysis using multispecies comparison. It takes as input a genomic sequence and a set of other sequences coming from a variety of species to be compared against the target sequences, and proceeds in four steps. CG-seq includes YASS and carnac software, and is also designed to run with BLAST and RNAz . By now, CG-seq is focused on noncoding RNAs. It could be extended to coding regions using Protea . CG-seq is available in a command-line version, and with a GUI written in Java. It is distributed under the GPL license.


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