密码子探索者：一款用于分析密码子使用情况和序列组成的在线工具，可从基因扩展到基因组。
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.
作者信息
Hamady Micah, Wilson Stephanie A, Zaneveld Jesse, Sueoka Noboru, Knight Rob
机构信息
Department of Computer Science, University of Colorado, Boulder, CO 80309, USA.
出版信息
Bioinformatics. 2009 May 15;25(10):1331-2. doi: 10.1093/bioinformatics/btp141. Epub 2009 Mar 11.
Abstract
DNA composition in general, and codon usage in particular, is crucial for understanding gene function and evolution. CodonExplorer, available online at http://bmf.colorado.edu/codonexplorer/, is an online tool and interactive database that contains millions of genes, allowing rapid exploration of the factors governing gene and genome compositional evolution and exploiting GC content and codon usage frequency to identify genes with composition suggesting high levels of expression or horizontal transfer.
摘要
一般而言，DNA组成，特别是密码子使用情况，对于理解基因功能和进化至关重要。CodonExplorer可在http://bmf.colorado.edu/codonexplorer/在线获取，它是一个在线工具和交互式数据库，包含数百万个基因，能够快速探究影响基因和基因组组成进化的因素，并利用GC含量和密码子使用频率来识别那些在组成上表明具有高表达水平或水平转移的基因。
相似文献
1
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.
Bioinformatics. 2009 May 15;25(10):1331-2. doi: 10.1093/bioinformatics/btp141. Epub 2009 Mar 11.
2
CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition.
Methods Mol Biol. 2009;537:207-32. doi: 10.1007/978-1-59745-251-9_10.
3
CodonO: codon usage bias analysis within and across genomes.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W132-6. doi: 10.1093/nar/gkm392. Epub 2007 May 30.
4
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes.
BMC Evol Biol. 2004 Jun 28;4:19. doi: 10.1186/1471-2148-4-19.
5
EuGene: maximizing synthetic gene design for heterologous expression.
Bioinformatics. 2012 Oct 15;28(20):2683-4. doi: 10.1093/bioinformatics/bts465. Epub 2012 Jul 30.
6
Compositional correlation and codon usage studies in Buchnera aphidicola.
Indian J Biochem Biophys. 2002 Feb;39(1):35-48.
7
The complete mitochondrial genome of the stomatopod crustacean Squilla mantis.
BMC Genomics. 2005 Aug 9;6:105. doi: 10.1186/1471-2164-6-105.
8
Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.
BMC Genomics. 2016 May 17;17:366. doi: 10.1186/s12864-016-2692-4.
9
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes.
Genome Biol. 2001;2(4):RESEARCH0010. doi: 10.1186/gb-2001-2-4-research0010. Epub 2001 Mar 22.
10
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.
Nucleic Acids Res. 2003 Jan 1;31(1):187-9. doi: 10.1093/nar/gkg004.
引用本文的文献
1
Codon-based indices for modeling gene expression and transcript evolution.
Comput Struct Biotechnol J. 2021 Apr 22;19:2646-2663. doi: 10.1016/j.csbj.2021.04.042. eCollection 2021.
2
CBDB: the codon bias database.
BMC Bioinformatics. 2012 Apr 26;13:62. doi: 10.1186/1471-2105-13-62.
本文引用的文献
1
PyCogent: a toolkit for making sense from sequence.
Genome Biol. 2007;8(8):R171. doi: 10.1186/gb-2007-8-8-r171.
2
Compositional correlation between deoxyribonucleic acid and protein.
Cold Spring Harb Symp Quant Biol. 1961;26:35-43. doi: 10.1101/sqb.1961.026.01.009.
3
Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses.
Gene. 2002 Oct 30;300(1-2):141-54. doi: 10.1016/s0378-1119(02)01046-6.
4
Asymmetric directional mutation pressures in bacteria.
Genome Biol. 2002 Sep 26;3(10):RESEARCH0058. doi: 10.1186/gb-2002-3-10-research0058.
5
Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa.
Gene. 2001 Jul 25;273(1):63-70. doi: 10.1016/s0378-1119(01)00576-5.
6
Codon usages in different gene classes of the Escherichia coli genome.
Mol Microbiol. 1998 Sep;29(6):1341-55. doi: 10.1046/j.1365-2958.1998.01008.x.
7
The vertebrate genome: isochores and evolution.
Mol Biol Evol. 1993 Jan;10(1):186-204. doi: 10.1093/oxfordjournals.molbev.a039994.
8
Intrastrand parity rules of DNA base composition and usage biases of synonymous codons.
J Mol Evol. 1995 Mar;40(3):318-25. doi: 10.1007/BF00163236.
9
Separation of microbial deoxyribonucleic acids into complementary strands.
Proc Natl Acad Sci U S A. 1969 May;63(1):152-9. doi: 10.1073/pnas.63.1.152.
10
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95. doi: 10.1093/nar/15.3.1281.
Zotero 插件