[Gene prediction and function research of SARS-CoV(BJ01)].
Identifieur interne : 000516 ( Ncbi/Curation ); précédent : 000515; suivant : 000517[Gene prediction and function research of SARS-CoV(BJ01)].
Auteurs : Ting-Gui Chen [République populaire de Chine] ; Song-Feng Wu ; Ping Wan ; Chun-Juan Du ; Jian-Qi Li ; Dong Li ; Guang-Zhi Wei ; Bin Li ; Zhong-Sheng Wang ; Xiao-Fang Xue ; Yun-Ping Zhu ; Fu-Chu HeSource :
- Yi chuan xue bao = Acta genetica Sinica [ 0379-4172 ] ; 2003.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Genes, Viral, Open Reading Frames, SARS Virus.
- methods : Computational Biology.
- Reproducibility of Results.
Abstract
Through reading the articles, this study points out the shortage of gene prediction and function research about SARS-CoV, and predict it again for developing effective drugs and future vaccines. Using twelve gene prediction methods to predict coronavirus known genes, we select four better methods including Heuristic models, Gene Identification, ZCURVE_CoV and ORF FINDER to predict SARS-CoV(BJ01), and use ATGpr for analyzing probability of initiation codon and Kozak rule, search transcription regulating sequence(TRS) in order to improve the accuracy of predicted genes. Twenty-one probable new genes with more than 50 amino acids have been obtained excluding 13 ORFs which are similar to the genes of NCBI and relative articles. For predicted proteins, we use ProtParam to analyse physical and chemical features; SignalP to analyse signal peptide; BLAST, FASTA to search similar sequences; TMPred, TMHMM, PFAM and HMMTOP to analyse domain and motif in order to improve reliability of gene function prediction. At the same time, we separate the 21 ORFs into four classes using codition of four gene prediction methods, match score, match expection and match length between predicted gene and Coronavirus known gene. In the end, we discuss the results and analyse the reasons.
PubMed: 14682248
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :003033
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :003033
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :002F40
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000516
Links to Exploration step
pubmed:14682248Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">[Gene prediction and function research of SARS-CoV(BJ01)].</title>
<author><name sortKey="Chen, Ting Gui" sort="Chen, Ting Gui" uniqKey="Chen T" first="Ting-Gui" last="Chen">Ting-Gui Chen</name>
<affiliation wicri:level="1"><nlm:affiliation>Laboratory of Systems Biology, Beijing Institute of Radiation Medicine, Beijing 100850, China. chentg@hupo.org.cn</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Laboratory of Systems Biology, Beijing Institute of Radiation Medicine, Beijing 100850</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wu, Song Feng" sort="Wu, Song Feng" uniqKey="Wu S" first="Song-Feng" last="Wu">Song-Feng Wu</name>
</author>
<author><name sortKey="Wan, Ping" sort="Wan, Ping" uniqKey="Wan P" first="Ping" last="Wan">Ping Wan</name>
</author>
<author><name sortKey="Du, Chun Juan" sort="Du, Chun Juan" uniqKey="Du C" first="Chun-Juan" last="Du">Chun-Juan Du</name>
</author>
<author><name sortKey="Li, Jian Qi" sort="Li, Jian Qi" uniqKey="Li J" first="Jian-Qi" last="Li">Jian-Qi Li</name>
</author>
<author><name sortKey="Li, Dong" sort="Li, Dong" uniqKey="Li D" first="Dong" last="Li">Dong Li</name>
</author>
<author><name sortKey="Wei, Guang Zhi" sort="Wei, Guang Zhi" uniqKey="Wei G" first="Guang-Zhi" last="Wei">Guang-Zhi Wei</name>
</author>
<author><name sortKey="Li, Bin" sort="Li, Bin" uniqKey="Li B" first="Bin" last="Li">Bin Li</name>
</author>
<author><name sortKey="Wang, Zhong Sheng" sort="Wang, Zhong Sheng" uniqKey="Wang Z" first="Zhong-Sheng" last="Wang">Zhong-Sheng Wang</name>
</author>
<author><name sortKey="Xue, Xiao Fang" sort="Xue, Xiao Fang" uniqKey="Xue X" first="Xiao-Fang" last="Xue">Xiao-Fang Xue</name>
</author>
<author><name sortKey="Zhu, Yun Ping" sort="Zhu, Yun Ping" uniqKey="Zhu Y" first="Yun-Ping" last="Zhu">Yun-Ping Zhu</name>
</author>
<author><name sortKey="He, Fu Chu" sort="He, Fu Chu" uniqKey="He F" first="Fu-Chu" last="He">Fu-Chu He</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2003">2003</date>
<idno type="RBID">pubmed:14682248</idno>
<idno type="pmid">14682248</idno>
<idno type="wicri:Area/PubMed/Corpus">003033</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003033</idno>
<idno type="wicri:Area/PubMed/Curation">003033</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003033</idno>
<idno type="wicri:Area/PubMed/Checkpoint">002F40</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002F40</idno>
<idno type="wicri:Area/Ncbi/Merge">000516</idno>
<idno type="wicri:Area/Ncbi/Curation">000516</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">[Gene prediction and function research of SARS-CoV(BJ01)].</title>
<author><name sortKey="Chen, Ting Gui" sort="Chen, Ting Gui" uniqKey="Chen T" first="Ting-Gui" last="Chen">Ting-Gui Chen</name>
<affiliation wicri:level="1"><nlm:affiliation>Laboratory of Systems Biology, Beijing Institute of Radiation Medicine, Beijing 100850, China. chentg@hupo.org.cn</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Laboratory of Systems Biology, Beijing Institute of Radiation Medicine, Beijing 100850</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wu, Song Feng" sort="Wu, Song Feng" uniqKey="Wu S" first="Song-Feng" last="Wu">Song-Feng Wu</name>
</author>
<author><name sortKey="Wan, Ping" sort="Wan, Ping" uniqKey="Wan P" first="Ping" last="Wan">Ping Wan</name>
</author>
<author><name sortKey="Du, Chun Juan" sort="Du, Chun Juan" uniqKey="Du C" first="Chun-Juan" last="Du">Chun-Juan Du</name>
</author>
<author><name sortKey="Li, Jian Qi" sort="Li, Jian Qi" uniqKey="Li J" first="Jian-Qi" last="Li">Jian-Qi Li</name>
</author>
<author><name sortKey="Li, Dong" sort="Li, Dong" uniqKey="Li D" first="Dong" last="Li">Dong Li</name>
</author>
<author><name sortKey="Wei, Guang Zhi" sort="Wei, Guang Zhi" uniqKey="Wei G" first="Guang-Zhi" last="Wei">Guang-Zhi Wei</name>
</author>
<author><name sortKey="Li, Bin" sort="Li, Bin" uniqKey="Li B" first="Bin" last="Li">Bin Li</name>
</author>
<author><name sortKey="Wang, Zhong Sheng" sort="Wang, Zhong Sheng" uniqKey="Wang Z" first="Zhong-Sheng" last="Wang">Zhong-Sheng Wang</name>
</author>
<author><name sortKey="Xue, Xiao Fang" sort="Xue, Xiao Fang" uniqKey="Xue X" first="Xiao-Fang" last="Xue">Xiao-Fang Xue</name>
</author>
<author><name sortKey="Zhu, Yun Ping" sort="Zhu, Yun Ping" uniqKey="Zhu Y" first="Yun-Ping" last="Zhu">Yun-Ping Zhu</name>
</author>
<author><name sortKey="He, Fu Chu" sort="He, Fu Chu" uniqKey="He F" first="Fu-Chu" last="He">Fu-Chu He</name>
</author>
</analytic>
<series><title level="j">Yi chuan xue bao = Acta genetica Sinica</title>
<idno type="ISSN">0379-4172</idno>
<imprint><date when="2003" type="published">2003</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term>
<term>Genes, Viral (genetics)</term>
<term>Open Reading Frames (genetics)</term>
<term>Reproducibility of Results</term>
<term>SARS Virus (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique ()</term>
<term>Cadres ouverts de lecture (génétique)</term>
<term>Gènes viraux (génétique)</term>
<term>Reproductibilité des résultats</term>
<term>Virus du SRAS (génétique)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genes, Viral</term>
<term>Open Reading Frames</term>
<term>SARS Virus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cadres ouverts de lecture</term>
<term>Gènes viraux</term>
<term>Virus du SRAS</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Reproducibility of Results</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term>
<term>Reproductibilité des résultats</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Through reading the articles, this study points out the shortage of gene prediction and function research about SARS-CoV, and predict it again for developing effective drugs and future vaccines. Using twelve gene prediction methods to predict coronavirus known genes, we select four better methods including Heuristic models, Gene Identification, ZCURVE_CoV and ORF FINDER to predict SARS-CoV(BJ01), and use ATGpr for analyzing probability of initiation codon and Kozak rule, search transcription regulating sequence(TRS) in order to improve the accuracy of predicted genes. Twenty-one probable new genes with more than 50 amino acids have been obtained excluding 13 ORFs which are similar to the genes of NCBI and relative articles. For predicted proteins, we use ProtParam to analyse physical and chemical features; SignalP to analyse signal peptide; BLAST, FASTA to search similar sequences; TMPred, TMHMM, PFAM and HMMTOP to analyse domain and motif in order to improve reliability of gene function prediction. At the same time, we separate the 21 ORFs into four classes using codition of four gene prediction methods, match score, match expection and match length between predicted gene and Coronavirus known gene. In the end, we discuss the results and analyse the reasons.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000516 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 000516 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= SrasV1 |flux= Ncbi |étape= Curation |type= RBID |clé= pubmed:14682248 |texte= [Gene prediction and function research of SARS-CoV(BJ01)]. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:14682248" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \ | NlmPubMed2Wicri -a SrasV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |