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Frontiers news briefs: May 23
Date:5/23/2013

Frontiers in Plant Science

Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

Within the genome of each species, there are thousands of stretches of DNA that undergo little change in position and sequence over millions of years, but do not code for any proteins. Some of these evolutionarily stable sequences, so-called conserved noncoding sequences (CNSs), are known to regulate the expression of other genes or the condensation of chromosomes, but the function of many CNSs remains unknown. Michael Freeling and colleagues from Berkeley here present their new open-source program "CNS Discovery Pipeline 3.0" which has taken three programmers six years to develop and can automatically find CNSs in newly sequenced genomes. The authors show that the program gives highly accurate results in a short time, requiring only 30 minutes to find the same number of CNSs as two trained biologists could do in two years. By helping us to understand how key genes are regulated, the program's output can boost medicine and the breeding of new crops.

URL: http://www.frontiersin.org/Plant_Genetics_and_Genomics/10.3389/fpls.2013.00170/abstract

Source code for CNS Discovery Pipeline 3.0 at: https://github.com/gturco/find_cns

Instructions for installation at: https://github.com/gturco/find_cns/blob/master/INSTALL.rst

Researcher contact

Prof Michael Freeling
Department of Plant & Microbial Biology
University of California at Berkeley
Email: freeling@berkeley.edu


Frontiers in Behavioral Neuroscie
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Contact: Gozde Zorlu
gozde.zorlu@frontiersin.org
Frontiers
Source:Eurekalert

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