Literature DB >> 15374859

Online synonymous codon usage analyses with the ade4 and seqinR packages.

D Charif1, J Thioulouse, J R Lobry, G Perrière.   

Abstract

UNLABELLED: 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: 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. CONTACT: http://pbil.univ-lyon1.fr/members/lobry.

Entities:  

Mesh：

Substances：

Year:  2004        PMID： 15374859     DOI： 10.1093/bioinformatics/bti037

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  35 in total

1.  The GDNF target Vsnl1 marks the ureteric tip.

Authors:  Roxana Ola; Madis Jakobson; Jouni Kvist; Nina Perälä; Satu Kuure; Karl-Heinz Braunewell; Darren Bridgewater; Norman D Rosenblum; Dmitri Chilov; Tiina Immonen; Kirsi Sainio; Hannu Sariola
Journal:  J Am Soc Nephrol       Date:  2011-02       Impact factor: 10.121

2.  In silico characterization and comparative genomic analysis of the Culex quinquefasciatus glutathione S-transferase (GST) supergene family.

Authors:  B P Niranjan Reddy; G B K S Prasad; K Raghavendra
Journal:  Parasitol Res       Date:  2011-04-15       Impact factor: 2.289

3.  HIV-1 Protease Evolvability Is Affected by Synonymous Nucleotide Recoding.

Authors:  Maria Nevot; Ana Jordan-Paiz; Glòria Martrus; Cristina Andrés; Damir García-Cehic; Josep Gregori; Sandra Franco; Josep Quer; Miguel Angel Martinez
Journal:  J Virol       Date:  2018-07-31       Impact factor: 5.103

4.  Sharing Programming Resources Between Bio* Projects.

Authors:  Raoul J P Bonnal; Andrew Yates; Naohisa Goto; Laurent Gautier; Scooter Willis; Christopher Fields; Toshiaki Katayama; Pjotr Prins
Journal:  Methods Mol Biol       Date:  2019

5.  Demasculinization of X chromosomes in the Drosophila genus.

Authors:  David Sturgill; Yu Zhang; Michael Parisi; Brian Oliver
Journal:  Nature       Date:  2007-11-08       Impact factor: 49.962

6.  Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes.

Authors:  Heidrun Sigrid Windisch; Magnus Lucassen; Stephan Frickenhaus
Journal:  BMC Genomics       Date:  2012-10-11       Impact factor: 3.969

7.  Analysis and prediction of translation rate based on sequence and functional features of the mRNA.

Authors:  Tao Huang; Sibao Wan; Zhongping Xu; Yufang Zheng; Kai-Yan Feng; Hai-Peng Li; Xiangyin Kong; Yu-Dong Cai
Journal:  PLoS One       Date:  2011-01-06       Impact factor: 3.240

8.  Measure of synonymous codon usage diversity among genes in bacteria.

Authors:  Haruo Suzuki; Rintaro Saito; Masaru Tomita
Journal:  BMC Bioinformatics       Date:  2009-06-01       Impact factor: 3.169

9.  Comparison of correspondence analysis methods for synonymous codon usage in bacteria.

Authors:  Haruo Suzuki; Celeste J Brown; Larry J Forney; Eva M Top
Journal:  DNA Res       Date:  2008-10-21       Impact factor: 4.458

10.  Evolution of codon usage in the smallest photosynthetic eukaryotes and their giant viruses.

Authors:  Stephanie Michely; Eve Toulza; Lucie Subirana; Uwe John; Valérie Cognat; Laurence Maréchal-Drouard; Nigel Grimsley; Hervé Moreau; Gwenaël Piganeau
Journal:  Genome Biol Evol       Date:  2013       Impact factor: 3.416
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.