Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales
Identifieur interne : 005911 ( Main/Merge ); précédent : 005910; suivant : 005912Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales
Auteurs : Wanjun Gu ; Tong Zhou ; Jianmin Ma ; Xiao Sun ; Zuhong LuSource :
- Virus Research [ 0168-1702 ] ; 2004.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Codon.
- genetics : Nidovirales, SARS Virus.
- Base Composition, Evolution, Molecular, Genes, Viral, Mutation, Open Reading Frames, Phylogeny, Protein Biosynthesis.
Abstract
In this study, we calculated the codon usage bias in severe acute respiratory syndrome
Url:
DOI: 10.1016/j.virusres.2004.01.006
PubMed: 15041183
PubMed Central: 7127446
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 001584
- to stream Pmc, to step Curation: 001584
- to stream Pmc, to step Checkpoint: 001734
- to stream PubMed, to step Corpus: 002E88
- to stream PubMed, to step Curation: 002E88
- to stream PubMed, to step Checkpoint: 002E37
- to stream Ncbi, to step Merge: 000706
- to stream Ncbi, to step Curation: 000706
- to stream Ncbi, to step Checkpoint: 000706
Links to Exploration step
PMC:7127446Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Analysis of synonymous codon usage in SARS <italic>Coronavirus</italic> and other viruses in the <italic>Nidovirales</italic></title><author><name sortKey="Gu, Wanjun" sort="Gu, Wanjun" uniqKey="Gu W" first="Wanjun" last="Gu">Wanjun Gu</name></author><author><name sortKey="Zhou, Tong" sort="Zhou, Tong" uniqKey="Zhou T" first="Tong" last="Zhou">Tong Zhou</name></author><author><name sortKey="Ma, Jianmin" sort="Ma, Jianmin" uniqKey="Ma J" first="Jianmin" last="Ma">Jianmin Ma</name></author><author><name sortKey="Sun, Xiao" sort="Sun, Xiao" uniqKey="Sun X" first="Xiao" last="Sun">Xiao Sun</name></author><author><name sortKey="Lu, Zuhong" sort="Lu, Zuhong" uniqKey="Lu Z" first="Zuhong" last="Lu">Zuhong Lu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">15041183</idno><idno type="pmc">7127446</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7127446</idno><idno type="RBID">PMC:7127446</idno><idno type="doi">10.1016/j.virusres.2004.01.006</idno><date when="2004">2004</date><idno type="wicri:Area/Pmc/Corpus">001584</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001584</idno><idno type="wicri:Area/Pmc/Curation">001584</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001584</idno><idno type="wicri:Area/Pmc/Checkpoint">001734</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001734</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:15041183</idno><idno type="wicri:Area/PubMed/Corpus">002E88</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002E88</idno><idno type="wicri:Area/PubMed/Curation">002E88</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002E88</idno><idno type="wicri:Area/PubMed/Checkpoint">002E37</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002E37</idno><idno type="wicri:Area/Ncbi/Merge">000706</idno><idno type="wicri:Area/Ncbi/Curation">000706</idno><idno type="wicri:Area/Ncbi/Checkpoint">000706</idno><idno type="wicri:doubleKey">0168-1702:2004:Gu W:analysis:of:synonymous</idno><idno type="wicri:Area/Main/Merge">005911</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Analysis of synonymous codon usage in SARS <italic>Coronavirus</italic> and other viruses in the <italic>Nidovirales</italic></title><author><name sortKey="Gu, Wanjun" sort="Gu, Wanjun" uniqKey="Gu W" first="Wanjun" last="Gu">Wanjun Gu</name></author><author><name sortKey="Zhou, Tong" sort="Zhou, Tong" uniqKey="Zhou T" first="Tong" last="Zhou">Tong Zhou</name></author><author><name sortKey="Ma, Jianmin" sort="Ma, Jianmin" uniqKey="Ma J" first="Jianmin" last="Ma">Jianmin Ma</name></author><author><name sortKey="Sun, Xiao" sort="Sun, Xiao" uniqKey="Sun X" first="Xiao" last="Sun">Xiao Sun</name></author><author><name sortKey="Lu, Zuhong" sort="Lu, Zuhong" uniqKey="Lu Z" first="Zuhong" last="Lu">Zuhong Lu</name></author></analytic><series><title level="j">Virus Research</title><idno type="ISSN">0168-1702</idno><idno type="eISSN">1872-7492</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>Codon (genetics)</term><term>Evolution, Molecular</term><term>Genes, Viral</term><term>Mutation</term><term>Nidovirales (genetics)</term><term>Open Reading Frames</term><term>Phylogeny</term><term>Protein Biosynthesis</term><term>SARS Virus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biosynthèse des protéines</term><term>Cadres ouverts de lecture</term><term>Codon (génétique)</term><term>Composition en bases nucléiques</term><term>Gènes viraux</term><term>Mutation</term><term>Nidovirales (génétique)</term><term>Phylogénie</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Codon</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nidovirales</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Codon</term><term>Nidovirales</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Evolution, Molecular</term><term>Genes, Viral</term><term>Mutation</term><term>Open Reading Frames</term><term>Phylogeny</term><term>Protein Biosynthesis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biosynthèse des protéines</term><term>Cadres ouverts de lecture</term><term>Composition en bases nucléiques</term><term>Gènes viraux</term><term>Mutation</term><term>Phylogénie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In this study, we calculated the codon usage bias in severe acute respiratory syndrome <italic>Coronavirus</italic> (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the <italic>Nidovirales</italic>. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of <italic>Coronavirus</italic>. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chan Yeung, M" uniqKey="Chan Yeung M">M Chan-Yeung</name></author><author><name sortKey="Yu, W C" uniqKey="Yu W">W.C Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chiapello, H" uniqKey="Chiapello H">H Chiapello</name></author><author><name sortKey="Lisacek, F" uniqKey="Lisacek F">F Lisacek</name></author><author><name sortKey="Caboche, M" uniqKey="Caboche M">M Caboche</name></author><author><name sortKey="Henaut, A" uniqKey="Henaut A">A Henaut</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chiapello, H" uniqKey="Chiapello H">H Chiapello</name></author><author><name sortKey="Ollivier, E" uniqKey="Ollivier E">E Ollivier</name></author><author><name sortKey="Landes Devauchelle, C" uniqKey="Landes Devauchelle C">C Landes-Devauchelle</name></author><author><name sortKey="Nitschke, P" uniqKey="Nitschke P">P Nitschke</name></author><author><name sortKey="Risler, J L" uniqKey="Risler J">J.L Risler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chiusano, M L" uniqKey="Chiusano M">M.L Chiusano</name></author><author><name sortKey="D Nofrio, G" uniqKey="D Nofrio G">G D’Onofrio</name></author><author><name sortKey="Alvarez Valin, F" uniqKey="Alvarez Valin F">F Alvarez-Valin</name></author><author><name sortKey="Jabbari, K" uniqKey="Jabbari K">K Jabbari</name></author><author><name sortKey="Colonna, G" uniqKey="Colonna G">G Colonna</name></author><author><name sortKey="Bernardi, G" uniqKey="Bernardi G">G Bernardi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chiusano, M L" uniqKey="Chiusano M">M.L Chiusano</name></author><author><name sortKey="Alvarez Valin, F" uniqKey="Alvarez Valin F">F Alvarez-Valin</name></author><author><name sortKey="Di Giulio, M" uniqKey="Di Giulio M">M Di Giulio</name></author><author><name sortKey="D Nofrio, G" uniqKey="D Nofrio G">G D’Onofrio</name></author><author><name sortKey="Ammirato, G" uniqKey="Ammirato G">G Ammirato</name></author><author><name sortKey="Colonna, G" uniqKey="Colonna G">G Colonna</name></author><author><name sortKey="Bernardi, G" uniqKey="Bernardi G">G Bernardi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coghlan, A" uniqKey="Coghlan A">A Coghlan</name></author><author><name sortKey="Wolfe, K H" uniqKey="Wolfe K">K.H Wolfe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Comeron, J M" uniqKey="Comeron J">J.M Comeron</name></author><author><name sortKey="Aguade, M" uniqKey="Aguade M">M Aguade</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drake, J W" uniqKey="Drake J">J.W Drake</name></author><author><name sortKey="Holland, J J" uniqKey="Holland J">J.J Holland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drazen, J M" uniqKey="Drazen J">J.M Drazen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Epstein, R J" uniqKey="Epstein R">R.J Epstein</name></author><author><name sortKey="Lin, K" uniqKey="Lin K">K Lin</name></author><author><name sortKey="Tan, T W" uniqKey="Tan T">T.W Tan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Francino, H P" uniqKey="Francino H">H.P Francino</name></author><author><name sortKey="Ochman, H" uniqKey="Ochman H">H Ochman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ghosh, T C" uniqKey="Ghosh T">T.C Ghosh</name></author><author><name sortKey="Gupta, S K" uniqKey="Gupta S">S.K Gupta</name></author><author><name sortKey="Majumdar, S" uniqKey="Majumdar S">S Majumdar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gouy, M" uniqKey="Gouy M">M Gouy</name></author><author><name sortKey="Gautier, C" uniqKey="Gautier C">C Gautier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grantham, R" uniqKey="Grantham R">R Grantham</name></author><author><name sortKey="Gautier, C" uniqKey="Gautier C">C Gautier</name></author><author><name sortKey="Gouy, M" uniqKey="Gouy M">M Gouy</name></author><author><name sortKey="Mercier, R" uniqKey="Mercier R">R Mercier</name></author><author><name sortKey="Pave, A" uniqKey="Pave A">A Pave</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grantham, R" uniqKey="Grantham R">R Grantham</name></author><author><name sortKey="Gautier, C" uniqKey="Gautier C">C Gautier</name></author><author><name sortKey="Gouy, M" uniqKey="Gouy M">M Gouy</name></author><author><name sortKey="Jacobzone, M" uniqKey="Jacobzone M">M Jacobzone</name></author><author><name sortKey="Mercier, R" uniqKey="Mercier R">R Mercier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gupta, S K" uniqKey="Gupta S">S.K Gupta</name></author><author><name sortKey="Majumdar, S" uniqKey="Majumdar S">S Majumdar</name></author><author><name sortKey="Bhattacharya, T K" uniqKey="Bhattacharya T">T.K Bhattacharya</name></author><author><name sortKey="Ghosh, T C" uniqKey="Ghosh T">T.C Ghosh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ikemura, T" uniqKey="Ikemura T">T Ikemura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ikemura, T" uniqKey="Ikemura T">T Ikemura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jenkins, G M" uniqKey="Jenkins G">G.M Jenkins</name></author><author><name sortKey="Pagel, M" uniqKey="Pagel M">M Pagel</name></author><author><name sortKey="Gould, E A" uniqKey="Gould E">E.A Gould</name></author><author><name sortKey="Zanotto, P M D A" uniqKey="Zanotto P">P.M.d.A Zanotto</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C Holmes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jenkins, G M" uniqKey="Jenkins G">G.M Jenkins</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C Holmes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author><author><name sortKey="Mrazek, J" uniqKey="Mrazek J">J Mrazek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lesnik, T" uniqKey="Lesnik T">T Lesnik</name></author><author><name sortKey="Solomovici, J" uniqKey="Solomovici J">J Solomovici</name></author><author><name sortKey="Deana, A" uniqKey="Deana A">A Deana</name></author><author><name sortKey="Ehrlich, R" uniqKey="Ehrlich R">R Ehrlich</name></author><author><name sortKey="Reiss, C" uniqKey="Reiss C">C Reiss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levin, D B" uniqKey="Levin D">D.B Levin</name></author><author><name sortKey="Whittome, B" uniqKey="Whittome B">B Whittome</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lloyd, A T" uniqKey="Lloyd A">A.T Lloyd</name></author><author><name sortKey="Sharp, P M" uniqKey="Sharp P">P.M Sharp</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, J M" uniqKey="Ma J">J.M Ma</name></author><author><name sortKey="Zhou, T" uniqKey="Zhou T">T Zhou</name></author><author><name sortKey="Gu, W J" uniqKey="Gu W">W.J Gu</name></author><author><name sortKey="Sun, X" uniqKey="Sun X">X Sun</name></author><author><name sortKey="Lu, Z H" uniqKey="Lu Z">Z.H Lu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Majumdar, S" uniqKey="Majumdar S">S Majumdar</name></author><author><name sortKey="Gupta, S K" uniqKey="Gupta S">S.K Gupta</name></author><author><name sortKey="Sundararaj, V S" uniqKey="Sundararaj V">V.S Sundararaj</name></author><author><name sortKey="Ghosh, T C" uniqKey="Ghosh T">T.C Ghosh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marais, G" uniqKey="Marais G">G Marais</name></author><author><name sortKey="Duret, L" uniqKey="Duret L">L Duret</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Marra, M A" uniqKey="Marra M">M.A Marra</name></author><author><name sortKey="Jones, S J" uniqKey="Jones S">S.J Jones</name></author><author><name sortKey="Astell, C R" uniqKey="Astell C">C.R Astell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, A" uniqKey="Martin A">A Martin</name></author><author><name sortKey="Bertranpetit, J" uniqKey="Bertranpetit J">J Bertranpetit</name></author><author><name sortKey="Oliver, J L" uniqKey="Oliver J">J.L Oliver</name></author><author><name sortKey="Medina, J R" uniqKey="Medina J">J.R Medina</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcinerney, J O" uniqKey="Mcinerney J">J.O McInerney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moriyama, E N" uniqKey="Moriyama E">E.N Moriyama</name></author><author><name sortKey="Powell, J R" uniqKey="Powell J">J.R Powell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oresic, M" uniqKey="Oresic M">M Oresic</name></author><author><name sortKey="Shalloway, D" uniqKey="Shalloway D">D Shalloway</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paul, A R" uniqKey="Paul A">A.R Paul</name></author><author><name sortKey="Steven, O M" uniqKey="Steven O">O.M Steven</name></author><author><name sortKey="Stephan, S M" uniqKey="Stephan S">S.M Stephan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, E D" uniqKey="Qin E">E.D Qin</name></author><author><name sortKey="Zhu, Q Y" uniqKey="Zhu Q">Q.Y Zhu</name></author><author><name sortKey="Yu, M" uniqKey="Yu M">M Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sharp, P M" uniqKey="Sharp P">P.M Sharp</name></author><author><name sortKey="Li, W H" uniqKey="Li W">W.H Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sharp, P M" uniqKey="Sharp P">P.M Sharp</name></author><author><name sortKey="Tuohy, T M" uniqKey="Tuohy T">T.M Tuohy</name></author><author><name sortKey="Mosurski, K R" uniqKey="Mosurski K">K.R Mosurski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E.J Snijder</name></author><author><name sortKey="Bredenbeek, P J" uniqKey="Bredenbeek P">P.J Bredenbeek</name></author><author><name sortKey="Dobbe, J C" uniqKey="Dobbe J">J.C Dobbe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wright, F" uniqKey="Wright F">F Wright</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xie, T" uniqKey="Xie T">T Xie</name></author><author><name sortKey="Ding, D F" uniqKey="Ding D">D.F Ding</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 005911 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 005911 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= SrasV1
|flux= Main
|étape= Merge
|type= RBID
|clé= PMC:7127446
|texte= Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:15041183" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |