Online synonymous codon usage analyses with the ade4 and seqinR packages

Bioinformatics
D CharifG Perrière

Abstract

Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases. Availability through the Pole Bioinformatique Lyonnais (PBIL) Web server at http://pbil.univ-lyon1.fr/datasets/charif04/ with a demo allowing us to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence. http://pbil.univ-lyon1.fr/members/lobry.

References

Sep 1, 1985·Computer Applications in the Biosciences : CABIOS·M GouyG di Paola
Jun 20, 1998·Bioinformatics·J O McInerney
Oct 18, 2002·Nucleic Acids Research·Guy Perrière, Jean Thioulouse

❮ Previous
Next ❯

Citations

Aug 13, 2008·Journal of Molecular Evolution·Julien Dutheil
Nov 13, 2007·Nature·David SturgillBrian Oliver
Oct 23, 2008·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Haruo SuzukiEva M Top
Apr 9, 2013·Genome Biology and Evolution·Stephanie MichelyGwenaël Piganeau
Aug 15, 2012·Biological Reviews of the Cambridge Philosophical Society·Susanta K Behura, David W Severson
Mar 30, 2010·Conservation Biology : the Journal of the Society for Conservation Biology·Andrew T KnightBruce M Campbell
Jun 2, 2009·BMC Bioinformatics·Haruo SuzukiMasaru Tomita
Feb 4, 2011·Journal of the American Society of Nephrology : JASN·Roxana OlaHannu Sariola
Oct 31, 2013·Environmental Science and Pollution Research International·Zaher DriraLotfi Aleya
Sep 6, 2015·FEBS Letters·Hideo DohraHaruo Suzuki
Dec 15, 2010·Gene·Andrés IriarteHéctor Musto
Dec 9, 2009·Virus Research·Sourav Roychoudhury, Debaprasad Mukherjee
Sep 11, 2007·Biochimie·Manolo Gouy, Stéphane Delmotte
Jan 5, 2013·Microbiology·Andrés IriarteHéctor Musto
Sep 9, 2015·BMC Genomics·Sharanya ChatterjeeUtpal S Tatu
Sep 2, 2014·Current Biology : CB·Sophia AhmedSusana M Coelho
Sep 15, 2010·BMC Evolutionary Biology·Anne ChenuilSylvain Mousset
Jun 30, 2012·Gene·Andrés IriarteHéctor Musto
Sep 25, 2014·Frontiers in Genetics·Damien UlvelingFlorent Hubé
Oct 11, 2011·BMC Genetics·Paloma Morán, Andrés Pérez-Figueroa
May 11, 2011·BMC Evolutionary Biology·Kelly E O'QuinKaren L Carleton
Oct 12, 2010·PloS One·Mathieu GautierKatayoun Moazami-Goudarzi
Feb 7, 2015·PLoS Computational Biology·Hanna JulienneAlain Arneodo

❮ 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.