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Codon usage bias

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287:, a theory which posits that codon bias exists because of nonrandomness in the mutational patterns. In other words, some codons can undergo more changes and therefore result in lower equilibrium frequencies, also known as “rare” codons. Different organisms also exhibit different mutational biases, and there is growing evidence that the level of genome-wide GC content is the most significant parameter in explaining codon bias differences between organisms. Additional studies have demonstrated that codon biases can be statistically predicted in 20: 272:. Although it has been shown that the rate of amino acid incorporation at more frequent codons occurs at a much higher rate than that of rare codons, the speed of translation has not been shown to be directly affected and therefore the bias towards more frequent codons may not be directly advantageous. However, the increase in translation elongation speed may still be indirectly advantageous by increasing the cellular concentration of free 219:, codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons). However, this model does not seem to yet have experimental confirmation. Another problem is that the evolution of tRNA genes has been a very inactive area of research. 126:, as is indeed the case for the above-mentioned organisms. In other organisms that do not show high growing rates or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. Examples of this are 439:
regions. As a result, co-translational protein folding introduces several spatial and temporal constraints on the nascent polypeptide chain in its folding trajectory. Because mRNA translation rates are coupled to protein folding, and codon adaptation is linked to translation elongation, it has been
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enzymes preferentially use codons that are poorly adapted to normal tRNA abundances, but have codons that are adapted to tRNA pools under starvation conditions. Thus, codon usage can introduce an additional level of transcriptional regulation for appropriate gene expression under specific cellular
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hypothesized that manipulation at the sequence level may be an effective strategy to regulate or improve protein folding. Several studies have shown that pausing of translation as a result of local mRNA structure occurs for certain proteins, which may be necessary for proper folding. Furthermore,
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Generally speaking for highly expressed genes, translation elongation rates are faster along transcripts with higher codon adaptation to tRNA pools, and slower along transcripts with rare codons. This correlation between codon translation rates and cognate tRNA concentrations provides additional
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can lead to inefficient use and depletion of ribosomes and ultimately reduce levels of heterologous protein production. In addition, the composition of the gene (e.g. the total number of rare codons and the presence of consecutive rare codons) may also affect translation accuracy. However, using
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is degenerate. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others—that is, a greater frequency of one will be found than expected by chance. How such biases arise is a much debated area of
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There are 64 different codons (61 codons encoding for amino acids and 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the
91:, which contains two distinct databases, CoCoPUTs and TissueCoCoPUTs. Together, these two databases provide comprehensive, up-to-date codon, codon pair and dinucleotide usage statistics for all organisms with available sequence information and 52 human tissues, respectively. 489:, are widely used to analyze variations in codon usage among genes. There are many computer programs to implement the statistical analyses enumerated above, including CodonW, GCUA, INCA, etc. Codon optimization has applications in designing synthetic genes and 1822:
Ikemura T (September 1981). "Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system".
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modulation of translation elongation rates, which can provide several advantages to the organism. Specifically, codon usage can allow for global regulation of these rates, and rare codons may contribute to the accuracy of translation at the expense of speed.
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The nature of the codon usage-tRNA optimization has been fiercely debated. It is not clear whether codon usage drives tRNA evolution or vice versa. At least one mathematical model has been developed where both codon usage and tRNA expression co-evolve in
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codons that are optimized for tRNA pools in a particular host to overexpress a heterologous gene may also cause amino acid starvation and alter the equilibrium of tRNA pools. This method of adjusting codons to match host tRNA abundances, called
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Alexaki, Aikaterini; Kames, Jacob; Holcomb, David D.; Athey, John; Santana-Quintero, Luis V.; Lam, Phuc Vihn Nguyen; Hamasaki-Katagiri, Nobuko; Osipova, Ekaterina; Simonyan, Vahan; Bar, Haim; Komar, Anton A.; Kimchi-Sarfaty, Chava (June 2019).
384:, has traditionally been used for expression of a heterologous gene. However, new strategies for optimization of heterologous expression consider global nucleotide content such as local mRNA folding, codon pair bias, a codon ramp, 610:
Kames, Jacob; Alexaki, Aikaterini; Holcomb, David D.; Santana-Quintero, Luis V.; Athey, John C.; Hamasaki-Katagiri, Nobuko; Katneni, Upendra; Golikov, Anton; Ibla, Juan C.; Bar, Haim; Kimchi-Sarfaty, Chava (January 2020).
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Correddu, D.; Montaño López, J. d. J.; Angermayr, S. A.; Middleditch, M. J.; Payne, L. S.; Leung, I. K. H. (2019). "Effect of Consecutive Rare Codons on the Recombinant Production of Human Proteins in Escherichia coli".
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have been shown to have significant consequences in the folding process of the nascent protein and can even change substrate specificity of enzymes. These studies suggest that codon usage influences the speed at which
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regions can therefore play a major role in RNA secondary structure and downstream protein expression, which can undergo further selective pressures. In particular, strong secondary structure at the
122:(tRNA) pool. It is thought that optimal codons help to achieve faster translation rates and high accuracy. As a result of these factors, translational selection is expected to be stronger in highly 227:
Different factors have been proposed to be related to codon usage bias, including gene expression level (reflecting selection for optimizing the translation process by tRNA abundance),
465:, many statistical methods have been proposed and used to analyze codon usage bias. Methods such as the 'frequency of optimal codons' (Fop), the relative codon adaptation (RCA) or the 268:. The selectionist model also explains why more frequent codons are recognized by more abundant tRNA molecules, as well as the correlation between preferred codons, tRNA levels, and 260:
Although the mechanism of codon bias selection remains controversial, possible explanations for this bias fall into two general categories. One explanation revolves around the
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Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina; Rostovtsev, Alexandre; Santana-Quintero, Luis V.; Katneni, Upendra; Simonyan, Vahan; Kimchi-Sarfaty, Chava (2017-09-02).
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Kanaya, Shigehiko; Yamada, Yuko; Kudo, Yoshihiro; Ikemura, Toshimichi (1999). "Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of
773: 319:. It also suggests that selection is generally weak, but that selection intensity scales to higher expression and more functional constraints of coding sequences. 340:
of mRNA influences translational efficiency, synonymous changes at this region on the mRNA can result in profound effects on gene expression. Codon usage in
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and further supporting the mutation bias model. However, this model alone cannot fully explain why preferred codons are recognized by more abundant tRNAs.
315:. This hypothesis states that selection favors major codons over minor codons, but minor codons are able to persist due to mutation pressure and 838:
Sharp, Paul M.; Stenico, Michele; Peden, John F.; Lloyd, Andrew T. (1993). "Codon usage: mutational bias, translational selection, or both?".
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Mignon, C.; Mariano, N.; Stadthagen, G.; Lugari, A.; Lagoutte, P.; Donnat, S.; Chenavas, S.; Perot, C.; Sodoyer, R.; Werle, B. (2018).
732:"Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion" 449:
emerge vectorially from the ribosome, which may further impact protein folding pathways throughout the available structural space.
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and translation of a particular coding sequence can be less efficient when placed in a non-native context. For an overexpressed
1271:"Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus" 613:"TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression" 157: 1220:"Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes" 486: 654:"Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift" 1521:"Inhibition of translation by consecutive rare leucine codons in E. coli: absence of effect of varying mRNA stability" 247:, transcriptional selection, RNA stability, optimal growth temperature, hypersaline adaptation, and dietary nitrogen. 207:. The suggestion has been made that these codon biases play a role in the temporal regulation of their late proteins. 2143: 563:"Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design" 470: 2108: 264:, in which codon bias contributes to the efficiency and/or accuracy of protein expression and therefore undergoes 1912:"The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications" 389: 352:
can inhibit translation, and mRNA folding at the 5’ end generates a large amount of variation in protein levels.
375:, the corresponding mRNA makes a large percent of total cellular RNA, and the presence of rare codons along the 2148: 2128: 2098: 2041: 368: 232: 228: 114: 106:
for codons that are favorable in regard to translation. Optimal codons in fast-growing microorganisms, like
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tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis".
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L. Duret and N. Galtier (2009). "Biased gene conversion and the evolution of mammalian genomic landscapes".
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Novoa, E. M.; Ribas De Pouplana, L (2012). "Speeding with control: Codon usage, tRNAs, and ribosomes".
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N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret (2018).
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Comeron JM, Aguadé M (September 1998). "An evaluation of measures of synonymous codon usage bias".
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Bornelöv, Susanne; Selmi, Tommaso; Flad, Sophia; Dietmann, Sabine; Frye, Michaela (2019-06-07).
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It is generally acknowledged that codon biases reflect the contributions of 3 main factors:
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Shin, Young C.; Bischof, Georg F.; Lauer, William A.; Desrosiers, Ronald C. (2015-09-10).
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of a protein exits the translating ribosome and becomes solvent-exposed before its more
2013: 1988: 1884: 1859: 1748: 1723: 1696: 1671: 1545: 1520: 1413: 1387:"Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms" 1386: 1295: 1270: 1246: 1219: 1119: 1084: 1013: 978: 680: 653: 537: 510: 458: 296: 184: 1989:"Comparison of correspondence analysis methods for synonymous codon usage in bacteria" 1938: 1911: 1195: 1170: 1053: 898: 2137: 1907: 1836: 1610: 1362: 1319: 596: 341: 316: 277: 1808: 1320:"Replicational and transcriptional selection on codon usage in Borrelia burgdorferi" 481:
are used to measure codon usage evenness. Multivariate statistical methods, such as
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is used in many biotechnological applications, including protein production and
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and selection, the prevailing hypothesis for codon bias can be explained by the
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Proceedings of the National Academy of Sciences of the United States of America
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Organisms that show an intermediate level of codon usage optimization include
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reflecting mutational preferences (typically favoring AT-ending codons), and
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genome are co-adapted for optimal translation of highly expressed genes".
859: 824: 1186: 1171:"Synonymous codon usage is subject to selection in thermophilic bacteria" 388:
or codon correlations. With the number of nucleotide changes introduced,
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Online Synonymous Codon Usage Analyses with the ade4 and seqinR packages
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genes such as those involved in amino acid starvation. For example,
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Ermolaeva MD (October 2001). "Synonymous codon usage in bacteria".
367:. Because tRNA pools vary between different organisms, the rate of 2086: 928:
Atherton, John C.; Sharp, Paul M.; Lafay, Bénédicte (2000-04-01).
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scRCA - Automatic determination of translational codon usage bias
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Duret, Laurent (2000). "tRNA gene number and codon usage in the
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Hershberg, R; Petrov, D. A. (2008). "Selection on codon bias".
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is often necessary for the creation of such an optimized gene.
2048:: estimating codon usage bias and its statistical significance 979:"Codon usage optimization in pluripotent embryonic stem cells" 791:(1996). "Co-variation of tRNA abundance and codon usage in 283:
The second explanation for codon usage can be explained by
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that display heavily skewed codon usage compared to the
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refers to differences in the frequency of occurrence of
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Suzuki H, Brown CJ, Forney LJ, Top EM (December 2008).
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CAIcal -Set of tools to assess codon usage adaptation
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Genetic Algorithm Simulation for Codon Optimization
1218:Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008). 511:"A new and updated resource for codon usage tables" 98:that favors GC-ending codons in diploid organisms, 1728:Computational and Structural Biotechnology Journal 295:, arguing against the idea of selective forces on 2109:E-CAI - Expected value of Codon Adaptation Index 1665: 1663: 1519:Shu, P.; Dai, H.; Gao, W.; Goldman, E. (2006). 1436: 1434: 1432: 1324:Proceedings of the National Academy of Sciences 1089:Proceedings of the National Academy of Sciences 395:Specialized codon bias is further seen in some 1169:Lynn DJ, Singer GA, Hickey DA (October 2002). 8: 772:: CS1 maint: multiple names: authors list ( 276:and potentially the rate of initiation for 89:HIVE-Codon Usage Tables (HIVE-CUTs) project 2087:ACUA - Automated Codon Usage Analysis Tool 2082:INCA - Interactive Codon Analysis software 356:Effect on transcription or gene expression 2012: 1937: 1883: 1747: 1695: 1643: 1592: 1544: 1412: 1402: 1361: 1343: 1294: 1245: 1235: 1194: 1118: 1108: 1012: 994: 945: 757: 747: 679: 669: 628: 578: 536: 526: 408:Effect on speed of translation elongation 2104:HEG-DB - Highly Expressed Genes Database 2077:JCat - Java Codon Usage Adaptation Tool 1717: 1715: 501: 1967:Correspondence Analysis of Codon Usage 1722:Spencer, P. S.; Barral, J. M. (2012). 1455:10.1146/annurev.genet.42.110807.091442 765: 313:mutation-selection-drift balance model 303:Mutation-selection-drift balance model 7: 2099:OPTIMIZER - Codon usage optimization 1385:Seward, Emily; Kelly, Steve (2016). 1269:Kober, K. M.; Pogson, G. H. (2013). 652:P. Shah and M. A. Gilchrist (2011). 307:To reconcile the evidence from both 50:(a triplet) that encodes a specific 2067:GCUA - General Codon Usage Analysis 717:10.1146/annurev-genom-082908-150001 1318:McInerney, James O. (1998-09-01). 14: 1670:Plotkin, J. B.; Kudla, G (2011). 328:Effect on RNA secondary structure 323:Consequences of codon composition 787:Dong, Hengjiang; Nilsson, Lars; 256:Mutational bias versus selection 58:chain or for the termination of 2052:HIVE-Codon Usage Table database 46:. A codon is a series of three 2072:Graphical Codon Usage Analyser 1: 1858:Fox JM, Erill I (June 2010). 1054:10.1016/s0168-9525(00)02041-2 899:10.1016/s0378-1119(99)00225-5 158:Strongylocentrotus purpuratus 2039:Composition Analysis Toolkit 1837:10.1016/0022-2836(81)90003-6 797:Journal of Molecular Biology 795:at different growth rates". 617:Journal of Molecular Biology 567:Journal of Molecular Biology 487:principal component analysis 361:Heterologous gene expression 705:Annu Rev Genomics Hum Genet 175:). Several viral families ( 2165: 1537:10.3727/000000006783991881 947:10.1099/00221287-146-4-851 471:effective number of codons 16:Genetic bias in coding DNA 1910:; Li, Wen-Hsiung (1987). 1498:10.1016/j.tig.2012.07.006 1443:Annual Review of Genetics 1404:10.1186/s13059-016-1087-9 996:10.1186/s13059-019-1726-z 630:10.1016/j.jmb.2020.01.011 580:10.1016/j.jmb.2019.04.021 528:10.1186/s12859-017-1793-7 417:Effect on protein folding 390:artificial gene synthesis 96:GC-biased gene conversion 1345:10.1073/pnas.95.18.10698 233:horizontal gene transfer 231:(GC content, reflecting 229:guanine-cytosine content 115:Saccharomyces cerevisiae 1676:Nature Reviews Genetics 1645:10.1002/1873-3468.13046 1237:10.1186/gb-2008-9-4-r70 1110:10.1073/pnas.1515387112 671:10.1073/pnas.1016719108 483:correspondence analysis 401:amino acid biosynthetic 241:amino acid conservation 142:Drosophila melanogaster 1961:Peden J (2005-04-15). 1917:Nucleic Acids Research 1740:10.5936/csbj.201204006 809:10.1006/jmbi.1996.0428 467:codon adaptation index 199:) are known to encode 148:Caenorhabditis elegans 29: 2005:10.1093/dnares/dsn028 1963:"Codon usage indices" 1930:10.1093/nar/15.3.1281 1876:10.1093/dnares/dsq012 1287:10.1534/g3.113.005769 749:10.1093/molbev/msy015 463:computational biology 365:metabolic engineering 346:ribosome-binding site 251:Evolutionary theories 237:guanine-cytosine skew 235:or mutational bias), 26:Physcomitrella patens 22: 2057:Codon Usage Database 1144:Curr Issues Mol Biol 442:synonymous mutations 309:mutational pressures 293:intergenic sequences 223:Contributing factors 168:Arabidopsis thaliana 87:can be found in the 23:Codon usage bias in 1785:1998JMolE..47..268C 1336:1998PNAS...9510698M 1330:(18): 10698–10703. 1101:2015PNAS..11214030S 1095:(45): 14030–14035. 840:Biochem. Soc. Trans 789:Kurland, Charles G. 453:Methods of analysis 386:codon harmonization 334:secondary structure 262:selectionist theory 201:structural proteins 135:Helicobacter pylori 77:molecular evolution 2092:2020-07-26 at the 2044:2020-07-26 at the 1793:10.1007/PL00006384 1486:Trends in Genetics 1187:10.1093/nar/gkf546 1042:Trends in Genetics 852:10.1042/bst0210835 759:20.500.12210/34500 515:BMC Bioinformatics 479:information theory 382:codon optimization 266:positive selection 245:protein hydropathy 30: 2144:Molecular biology 1175:Nucleic Acids Res 883:Bacillus subtilis 623:(11): 3369–3378. 573:(13): 2434–2441. 270:gene copy numbers 104:natural selection 2156: 2027: 2026: 2016: 1984: 1978: 1977: 1975: 1974: 1958: 1952: 1951: 1941: 1924:(3): 1281–1295. 1904: 1898: 1897: 1887: 1855: 1849: 1848: 1819: 1813: 1812: 1768: 1762: 1761: 1751: 1719: 1710: 1709: 1699: 1667: 1658: 1657: 1647: 1638:(9): 1554–1564. 1621: 1615: 1614: 1596: 1585:10.1002/iub.2162 1565: 1559: 1558: 1548: 1516: 1510: 1509: 1481: 1475: 1474: 1438: 1427: 1426: 1416: 1406: 1382: 1376: 1375: 1365: 1347: 1315: 1309: 1308: 1298: 1281:(7): 1069–1083. 1266: 1260: 1259: 1249: 1239: 1215: 1209: 1208: 1198: 1166: 1160: 1159: 1139: 1133: 1132: 1122: 1112: 1080: 1074: 1073: 1033: 1027: 1026: 1016: 998: 974: 968: 967: 949: 925: 919: 918: 878: 872: 871: 835: 829: 828: 793:Escherichia coli 784: 778: 777: 771: 763: 761: 751: 742:(5): 1092–1103. 727: 721: 720: 700: 694: 693: 683: 673: 649: 643: 642: 632: 607: 601: 600: 582: 557: 551: 550: 540: 530: 506: 457:In the field of 431:, such that the 350:initiation codon 109:Escherichia coli 33:Codon usage bias 2164: 2163: 2159: 2158: 2157: 2155: 2154: 2153: 2149:Gene expression 2134: 2133: 2094:Wayback Machine 2046:Wayback Machine 2035: 2030: 1986: 1985: 1981: 1972: 1970: 1960: 1959: 1955: 1906: 1905: 1901: 1857: 1856: 1852: 1821: 1820: 1816: 1770: 1769: 1765: 1721: 1720: 1713: 1688:10.1038/nrg2899 1669: 1668: 1661: 1623: 1622: 1618: 1567: 1566: 1562: 1518: 1517: 1513: 1483: 1482: 1478: 1440: 1439: 1430: 1384: 1383: 1379: 1317: 1316: 1312: 1268: 1267: 1263: 1217: 1216: 1212: 1168: 1167: 1163: 1141: 1140: 1136: 1082: 1081: 1077: 1035: 1034: 1030: 976: 975: 971: 927: 926: 922: 880: 879: 875: 837: 836: 832: 786: 785: 781: 764: 729: 728: 724: 702: 701: 697: 664:(25): 10231–6. 651: 650: 646: 609: 608: 604: 559: 558: 554: 508: 507: 503: 499: 475:Shannon entropy 455: 422:Protein folding 419: 410: 358: 330: 325: 305: 285:mutational bias 258: 253: 225: 124:expressed genes 17: 12: 11: 5: 2162: 2160: 2152: 2151: 2146: 2136: 2135: 2132: 2131: 2126: 2121: 2116: 2111: 2106: 2101: 2096: 2084: 2079: 2074: 2069: 2064: 2059: 2054: 2049: 2034: 2033:External links 2031: 2029: 2028: 1979: 1953: 1908:Sharp, Paul M. 1899: 1850: 1831:(3): 389–409. 1814: 1763: 1711: 1659: 1616: 1579:(2): 266–274. 1560: 1511: 1492:(11): 574–81. 1476: 1428: 1391:Genome Biology 1377: 1310: 1261: 1210: 1181:(19): 4272–7. 1161: 1134: 1075: 1048:(7): 287–289. 1028: 983:Genome Biology 969: 940:(4): 851–860. 920: 893:(1): 143–155. 873: 846:(4): 835–841. 830: 803:(5): 649–663. 779: 722: 695: 644: 602: 552: 500: 498: 495: 459:bioinformatics 454: 451: 418: 415: 409: 406: 357: 354: 329: 326: 324: 321: 304: 301: 297:coding regions 278:messenger RNAs 257: 254: 252: 249: 224: 221: 185:papillomavirus 100:arrival biases 15: 13: 10: 9: 6: 4: 3: 2: 2161: 2150: 2147: 2145: 2142: 2141: 2139: 2130: 2127: 2125: 2122: 2120: 2117: 2115: 2112: 2110: 2107: 2105: 2102: 2100: 2097: 2095: 2091: 2088: 2085: 2083: 2080: 2078: 2075: 2073: 2070: 2068: 2065: 2063: 2060: 2058: 2055: 2053: 2050: 2047: 2043: 2040: 2037: 2036: 2032: 2024: 2020: 2015: 2010: 2006: 2002: 1999:(6): 357–65. 1998: 1994: 1990: 1983: 1980: 1969:. SourceForge 1968: 1964: 1957: 1954: 1949: 1945: 1940: 1935: 1931: 1927: 1923: 1919: 1918: 1913: 1909: 1903: 1900: 1895: 1891: 1886: 1881: 1877: 1873: 1870:(3): 185–96. 1869: 1865: 1861: 1854: 1851: 1846: 1842: 1838: 1834: 1830: 1826: 1818: 1815: 1810: 1806: 1802: 1798: 1794: 1790: 1786: 1782: 1779:(3): 268–74. 1778: 1774: 1767: 1764: 1759: 1755: 1750: 1745: 1741: 1737: 1733: 1729: 1725: 1718: 1716: 1712: 1707: 1703: 1698: 1693: 1689: 1685: 1681: 1677: 1673: 1666: 1664: 1660: 1655: 1651: 1646: 1641: 1637: 1633: 1632: 1627: 1620: 1617: 1612: 1608: 1604: 1600: 1595: 1590: 1586: 1582: 1578: 1574: 1573: 1564: 1561: 1556: 1552: 1547: 1542: 1538: 1534: 1531:(2): 97–106. 1530: 1526: 1522: 1515: 1512: 1507: 1503: 1499: 1495: 1491: 1487: 1480: 1477: 1472: 1468: 1464: 1460: 1456: 1452: 1448: 1444: 1437: 1435: 1433: 1429: 1424: 1420: 1415: 1410: 1405: 1400: 1397:(226): 3–15. 1396: 1392: 1388: 1381: 1378: 1373: 1369: 1364: 1359: 1355: 1351: 1346: 1341: 1337: 1333: 1329: 1325: 1321: 1314: 1311: 1306: 1302: 1297: 1292: 1288: 1284: 1280: 1276: 1272: 1265: 1262: 1257: 1253: 1248: 1243: 1238: 1233: 1229: 1225: 1221: 1214: 1211: 1206: 1202: 1197: 1192: 1188: 1184: 1180: 1176: 1172: 1165: 1162: 1157: 1153: 1149: 1145: 1138: 1135: 1130: 1126: 1121: 1116: 1111: 1106: 1102: 1098: 1094: 1090: 1086: 1079: 1076: 1071: 1067: 1063: 1059: 1055: 1051: 1047: 1043: 1039: 1032: 1029: 1024: 1020: 1015: 1010: 1006: 1002: 997: 992: 988: 984: 980: 973: 970: 965: 961: 957: 953: 948: 943: 939: 935: 931: 924: 921: 916: 912: 908: 904: 900: 896: 892: 888: 884: 877: 874: 869: 865: 861: 857: 853: 849: 845: 841: 834: 831: 826: 822: 818: 814: 810: 806: 802: 798: 794: 790: 783: 780: 775: 769: 760: 755: 750: 745: 741: 737: 736:Mol Biol Evol 733: 726: 723: 718: 714: 710: 706: 699: 696: 691: 687: 682: 677: 672: 667: 663: 659: 655: 648: 645: 640: 636: 631: 626: 622: 618: 614: 606: 603: 598: 594: 590: 586: 581: 576: 572: 568: 564: 556: 553: 548: 544: 539: 534: 529: 524: 520: 516: 512: 505: 502: 496: 494: 492: 488: 484: 480: 476: 472: 468: 464: 460: 452: 450: 448: 443: 438: 434: 430: 426: 423: 416: 414: 407: 405: 402: 398: 393: 391: 387: 383: 378: 374: 370: 369:transcription 366: 362: 355: 353: 351: 347: 343: 342:noncoding DNA 339: 335: 327: 322: 320: 318: 317:genetic drift 314: 310: 302: 300: 298: 294: 290: 286: 281: 279: 275: 271: 267: 263: 255: 250: 248: 246: 242: 238: 234: 230: 222: 220: 218: 214: 208: 206: 202: 198: 194: 190: 186: 182: 178: 174: 170: 169: 164: 160: 159: 154: 150: 149: 145:(fruit fly), 144: 143: 138: 136: 131: 130: 125: 121: 117: 116: 111: 110: 105: 101: 97: 92: 90: 86: 82: 78: 73: 67: 65: 61: 57: 54:residue in a 53: 49: 45: 41: 38: 34: 28: 27: 21: 1996: 1992: 1982: 1971:. Retrieved 1966: 1956: 1921: 1915: 1902: 1867: 1863: 1853: 1828: 1825:J. Mol. Biol 1824: 1817: 1776: 1773:J. Mol. Evol 1772: 1766: 1731: 1727: 1682:(1): 32–42. 1679: 1675: 1635: 1631:FEBS Letters 1629: 1619: 1594:11343/286411 1576: 1570: 1563: 1528: 1524: 1514: 1489: 1485: 1479: 1446: 1442: 1394: 1390: 1380: 1327: 1323: 1313: 1278: 1274: 1264: 1227: 1223: 1213: 1178: 1174: 1164: 1147: 1143: 1137: 1092: 1088: 1078: 1045: 1041: 1037: 1031: 986: 982: 972: 937: 934:Microbiology 933: 923: 890: 886: 882: 876: 843: 839: 833: 800: 796: 792: 782: 768:cite journal 739: 735: 725: 708: 704: 698: 661: 657: 647: 620: 616: 605: 570: 566: 555: 521:(391): 391. 518: 514: 504: 491:DNA vaccines 456: 447:polypeptides 424: 420: 411: 404:conditions. 394: 359: 331: 312: 306: 284: 282: 261: 259: 226: 216: 209: 189:polyomavirus 166: 156: 146: 140: 133: 132:(human) and 129:Homo sapiens 127: 120:transfer RNA 113: 107: 93: 72:genetic code 68: 32: 31: 24: 1224:Genome Biol 1150:(4): 91–7. 711:: 285–311. 473:' (Nc) and 291:using only 289:prokaryotes 177:herpesvirus 173:thale cress 64:stop codons 60:translation 56:polypeptide 48:nucleotides 2138:Categories 1973:2010-10-20 1572:IUBMB Life 1449:: 287–99. 1230:(4): R70. 1038:C. elegans 989:(1): 119. 497:References 437:C-terminal 433:N-terminus 397:endogenous 377:transcript 197:parvovirus 193:adenovirus 181:lentivirus 163:sea urchin 151:(nematode 52:amino acid 44:coding DNA 37:synonymous 1611:202555575 1525:Gene Expr 1354:0027-8424 1062:0168-9525 1005:1474-760X 956:1350-0872 907:0378-1119 817:0022-2836 597:139104807 429:vectorial 373:transgene 280:(mRNAs). 274:ribosomes 215:fashion ( 205:host cell 2090:Archived 2042:Archived 2023:18940873 1894:20453079 1809:21862217 1758:24688635 1706:21102527 1654:29624661 1603:31509345 1555:17017124 1506:22921354 1463:18983258 1423:27842572 1305:23637123 1256:18397532 1205:12364606 1156:11719972 1129:26504241 1070:10858656 1023:31174582 964:10784043 915:10570992 690:21646514 639:31982380 589:31029701 547:28865429 332:Because 213:feedback 2014:2608848 1993:DNA Res 1948:3547335 1885:2885275 1864:DNA Res 1845:6175758 1801:9732453 1781:Bibcode 1749:3962081 1734:: 1–8. 1697:3074964 1546:6032470 1471:7085012 1414:5109750 1372:9724767 1332:Bibcode 1296:3704236 1247:2643941 1120:4653223 1097:Bibcode 1014:6555954 868:8582630 860:8132077 825:8709146 681:3121864 538:5581930 425:in vivo 336:of the 165:), and 81:GenBank 2062:CodonW 2021:  2011:  1946:  1939:340524 1936:  1892:  1882:  1843:  1807:  1799:  1756:  1746:  1704:  1694:  1652:  1609:  1601:  1553:  1543:  1504:  1469:  1461:  1421:  1411:  1370:  1360:  1352:  1303:  1293:  1254:  1244:  1203:  1196:140546 1193:  1154:  1127:  1117:  1068:  1060:  1021:  1011:  1003:  962:  954:  913:  905:  866:  858:  823:  815:  688:  678:  637:  595:  587:  545:  535:  338:5’ end 195:, and 85:RefSeq 40:codons 1805:S2CID 1607:S2CID 1467:S2CID 1363:27958 864:S2CID 593:S2CID 477:from 2019:PMID 1944:PMID 1890:PMID 1841:PMID 1797:PMID 1754:PMID 1702:PMID 1650:PMID 1599:PMID 1551:PMID 1502:PMID 1459:PMID 1419:PMID 1368:PMID 1350:ISSN 1301:PMID 1252:PMID 1201:PMID 1152:PMID 1125:PMID 1066:PMID 1058:ISSN 1019:PMID 1001:ISSN 960:PMID 952:ISSN 911:PMID 903:ISSN 887:Gene 856:PMID 821:PMID 813:ISSN 774:link 686:PMID 635:PMID 585:PMID 543:PMID 485:and 461:and 217:i.e. 153:worm 83:and 2009:PMC 2001:doi 1934:PMC 1926:doi 1880:PMC 1872:doi 1833:doi 1829:151 1789:doi 1744:PMC 1736:doi 1692:PMC 1684:doi 1640:doi 1636:592 1589:hdl 1581:doi 1541:PMC 1533:doi 1494:doi 1451:doi 1409:PMC 1399:doi 1358:PMC 1340:doi 1291:PMC 1283:doi 1242:PMC 1232:doi 1191:PMC 1183:doi 1115:PMC 1105:doi 1093:112 1050:doi 1009:PMC 991:doi 942:doi 938:146 895:doi 891:238 848:doi 805:doi 801:260 754:hdl 744:doi 713:doi 676:PMC 666:doi 662:108 625:doi 621:432 575:doi 571:431 533:PMC 523:doi 427:is 348:or 155:), 112:or 66:). 42:in 2140:: 2017:. 2007:. 1997:15 1995:. 1991:. 1965:. 1942:. 1932:. 1922:15 1920:. 1914:. 1888:. 1878:. 1868:17 1866:. 1862:. 1839:. 1827:. 1803:. 1795:. 1787:. 1777:47 1775:. 1752:. 1742:. 1730:. 1726:. 1714:^ 1700:. 1690:. 1680:12 1678:. 1674:. 1662:^ 1648:. 1634:. 1628:. 1605:. 1597:. 1587:. 1577:72 1575:. 1549:. 1539:. 1529:13 1527:. 1523:. 1500:. 1490:28 1488:. 1465:. 1457:. 1447:42 1445:. 1431:^ 1417:. 1407:. 1395:17 1393:. 1389:. 1366:. 1356:. 1348:. 1338:. 1328:95 1326:. 1322:. 1299:. 1289:. 1277:. 1275:G3 1273:. 1250:. 1240:. 1226:. 1222:. 1199:. 1189:. 1179:30 1177:. 1173:. 1146:. 1123:. 1113:. 1103:. 1091:. 1087:. 1064:. 1056:. 1046:16 1044:. 1017:. 1007:. 999:. 987:20 985:. 981:. 958:. 950:. 936:. 932:. 909:. 901:. 889:. 862:. 854:. 844:21 842:. 819:. 811:. 799:. 770:}} 766:{{ 752:. 740:35 738:. 734:. 709:10 707:. 684:. 674:. 660:. 656:. 633:. 619:. 615:. 591:. 583:. 569:. 565:. 541:. 531:. 519:18 517:. 513:. 243:, 191:, 187:, 183:, 179:, 2025:. 2003:: 1976:. 1950:. 1928:: 1896:. 1874:: 1847:. 1835:: 1811:. 1791:: 1783:: 1760:. 1738:: 1732:1 1708:. 1686:: 1656:. 1642:: 1613:. 1591:: 1583:: 1557:. 1535:: 1508:. 1496:: 1473:. 1453:: 1425:. 1401:: 1374:. 1342:: 1334:: 1307:. 1285:: 1279:3 1258:. 1234:: 1228:9 1207:. 1185:: 1158:. 1148:3 1131:. 1107:: 1099:: 1072:. 1052:: 1025:. 993:: 966:. 944:: 917:. 897:: 870:. 850:: 827:. 807:: 776:) 762:. 756:: 746:: 719:. 715:: 692:. 668:: 641:. 627:: 599:. 577:: 549:. 525:: 171:( 161:( 137:. 62:(

Index


Physcomitrella patens
synonymous
codons
coding DNA
nucleotides
amino acid
polypeptide
translation
stop codons
genetic code
molecular evolution
GenBank
RefSeq
HIVE-Codon Usage Tables (HIVE-CUTs) project
GC-biased gene conversion
arrival biases
natural selection
Escherichia coli
Saccharomyces cerevisiae
transfer RNA
expressed genes
Homo sapiens
Helicobacter pylori
Drosophila melanogaster
Caenorhabditis elegans
worm
Strongylocentrotus purpuratus
sea urchin
Arabidopsis thaliana

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