GAME: detecting cis-regulatory elements using a genetic algorithm

Bioinformatics
Zhi Wei, Shane Jensen

Abstract

Identification of a transcription factor binding sites is an important aspect of the analysis of genetic regulation. Many programs have been developed for the de novo discovery of a binding motif (collection of binding sites). Recently, a scoring function formulation was derived that allows for the comparison of discovered motifs from different programs [S.T. Jensen, X.S. Liu, Q. Zhou and J.S. Liu (2004) Stat. Sci., 19, 188-204.] A simple program, BioOptimizer, was proposed in [S.T. Jensen and J.S. Liu (2004) Bioinformatics, 20, 1557-1564.] that improved discovered motifs by optimizing a scoring function. However, BioOptimizer is a very simple algorithm that can only make local improvements upon an already discovered motif and so BioOptimizer can only be used in conjunction with other motif-finding software. We introduce software, GAME, which utilizes a genetic algorithm to find optimal motifs in DNA sequences. GAME evolves motifs with high fitness from a population of randomly generated starting motifs, which eliminate the reliance on additional motif-finding programs. In addition to using standard genetic operations, GAME also incorporates two additional operators that are specific to the motif discovery problem. We demonstra...Continue Reading

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
Feb 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·G D Stormo, G W Hartzell
Aug 1, 1995·Protein Science : a Publication of the Protein Society·A F NeuwaldC E Lawrence
Jul 14, 2001·Nucleic Acids Research·C M Klinge
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P BermanMichael B Eisen
Jul 11, 2003·Nature·Michael Levine, Robert Tjian
Jan 6, 2004·Nucleic Acids Research·Martin C FrithZhiping Weng
Feb 14, 2004·Bioinformatics·Shane T Jensen, Jun S Liu
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mayetri Gupta, Jun S Liu
Dec 31, 2005·Nucleic Acids Research·Enrique BlancoRoderic Guigó

❮ Previous
Next ❯

Citations

Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Leping Li
Mar 8, 2007·Bioinformatics·Leping LiRobert L Bass
May 8, 2007·Bioinformatics·Edward WijayaWing-Kin Sung
Aug 20, 2009·Bioinformatics·Matthieu Defrance, Jacques van Helden
Sep 11, 2009·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Alexei A Sharov, Minoru S H Ko
Nov 30, 2006·Nucleic Acids Research·Ian J Donaldson, Berthold Göttgens
Jul 19, 2013·Journal of Bioinformatics and Computational Biology·Yipu ZhangQiang Yu
Oct 9, 2009·BMC Bioinformatics·Tak-Ming ChanKin-Hong Lee
Dec 6, 2007·BMC Bioinformatics·Modan K Das, Ho-Kwok Dai
Dec 15, 2010·BioData Mining·Chengwei Lei, Jianhua Ruan
May 8, 2009·Genes & Genetic Systems·Fatemeh Zare-MirakabadBahram Goliaei
Jan 1, 2009·Advances and Applications in Bioinformatics and Chemistry : AABC·Junfeng LiuWeichung Joe Shih
May 23, 2012·Artificial Intelligence in Medicine·Chengpeng Bi
Feb 16, 2010·Journal of Theoretical Biology·Jia-wei Luo, Ting Wang
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David L González-ÁlvarezÁlvaro Rubio-Largo
May 9, 2014·IEEE Transactions on Neural Networks and Learning Systems·Dianhui Wang, Sarwar Tapan
Aug 1, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Chengpeng Bi
Oct 30, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gang LiKin-Hong Lee
Jun 13, 2015·IEEE Transactions on Neural Networks and Learning Systems·Sarwar Tapan, Dianhui Wang
May 8, 2015·Nature Protocols·Lawrence A KelleyMichael J E Sternberg
Feb 18, 2016·IEEE Transactions on Cybernetics·Ka-Chun WongYue Li
May 5, 2017·Bioinformatics and Biology Insights·Rogelio Alcántara-SilvaSilvia Carolina Galván
Dec 6, 2018·BioMed Research International·Nesrine SghaierAhmed Rebai
Nov 25, 2016·BioMed Research International·Yipu ZhangMaode Yan
Aug 6, 2021·Briefings in Bioinformatics·Stefano CastellanaTommaso Mazza

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.