CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

Nucleic Acids Research
Yu-Jian KangGe Gao

Abstract

With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.

References

Sep 11, 1982·Nucleic Acids Research·J W Fickett
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 6, 2001·Nature Reviews. Genetics·S R Eddy
May 3, 2006·Human Molecular Genetics·John S Mattick, Igor V Makunin
Dec 6, 2006·Nucleic Acids Research·Ken C PangJohn S Mattick
Nov 15, 2007·Nucleic Acids Research·Shunmin HeRunsheng Chen
Nov 29, 2008·Science·Julius BrenneckeGregory J Hannon
Jun 6, 2012·Annual Review of Biochemistry·John L Rinn, Howard Y Chang
Mar 19, 2013·Cell·Jeannie T Lee, Marisa S Bartolomei
Jul 25, 2013·Cellular and Molecular Life Sciences : CMLS·Masatoshi KitagawaTatsuya Ohhata
Jun 14, 2014·Brain Tumor Research and Treatment·Ju Young ParkJong Heon Kim
Oct 22, 2014·Nucleic Acids Research·Xiu Cheng QuekMarcel E Dinger
Mar 31, 2015·National Science Review·Xiang-Dong Fu
Nov 1, 2015·Methods in Molecular Biology·Emmanuel BoutetIoannis Xenarios
Dec 22, 2015·Nucleic Acids Research·Andrew YatesPaul Flicek
Jun 7, 2016·Nature Reviews. Genetics·Hans Ellegren, Nicolas Galtier

❮ Previous
Next ❯

Citations

Jul 17, 2018·Briefings in Bioinformatics·Seo-Won ChoiJin-Wu Nam
Jul 7, 2018·The Plant Journal : for Cell and Molecular Biology·Agnieszka A GoliczMohan B Singh
Mar 1, 2019·Briefings in Bioinformatics·Siyuan ChenChuang Ma
Feb 24, 2019·Molecular Systems Biology·Samuel Miravet-VerdeMaria Lluch-Senar
Sep 5, 2019·Cells·Yujing ChiJichun Yang
Jan 9, 2020·Genome Biology·Mahdi Moradi MarjanehJuliet D French
Feb 11, 2020·PLoS Computational Biology·Xiangying SunXinan H Yang
Mar 8, 2020·Genome Research·Logan J EverettTrudy F C Mackay
Jan 10, 2020·Clinical and Translational Science·Bianca D van GroenJ Steven Leeder
Jun 5, 2020·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Bolin WuWen Cheng
Jun 20, 2020·Biotechnology and Bioengineering·Krishna MotheramgariColin Clarke
May 4, 2018·BMC Genomics·Caitlin M A SimopoulosG Brian Golding
Jun 7, 2018·Nucleic Acids Research·Eric Augusto ItoFabrício Martins Lopes
Oct 26, 2018·Circulation Research·Phillip Grote, Reinier A Boon
Mar 7, 2019·Frontiers in Cardiovascular Medicine·Adam W TurnerClint L Miller
Aug 29, 2019·Frontiers in Genetics·Xuan ZhangChangning Liu
Nov 11, 2019·BMC Bioinformatics·Mengmeng Zhu, Michael Gribskov
Oct 18, 2019·Journal of Cellular Physiology·Zahra ArabsorkhiMohammad Reza Zali
Dec 13, 2019·Arteriosclerosis, Thrombosis, and Vascular Biology·John HungAndrew H Baker
Apr 4, 2020·Proceedings of the National Academy of Sciences of the United States of America·Marina AznaourovaLeon N Schulte

❮ 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.