MicroSyn: a user friendly tool for detection of microsynteny in a gene family.
Identifieur interne : 002D93 ( Main/Exploration ); précédent : 002D92; suivant : 002D94MicroSyn: a user friendly tool for detection of microsynteny in a gene family.
Auteurs : Bin Cai [République populaire de Chine] ; Xiaohan Yang ; Gerald A. Tuskan ; Zong-Ming ChengSource :
- BMC bioinformatics [ 1471-2105 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Plantes, Synténie, microARN.
- méthodes : Génomique.
- Analyse de séquence d'ADN, Données de séquences moléculaires, Logiciel, Phylogenèse.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MicroRNAs.
- classification : Plants.
- genetics : Plants, Synteny.
- methods : Genomics.
- Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Software.
Abstract
BACKGROUND
The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.
RESULTS
We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: http://fcsb.njau.edu.cn/microsyn/.
CONCLUSIONS
Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in Populus trichocarpa were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.
DOI: 10.1186/1471-2105-12-79
PubMed: 21418570
PubMed Central: PMC3072343
Affiliations:
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Tuskan</name></author><author><name sortKey="Cheng, Zong Ming" sort="Cheng, Zong Ming" uniqKey="Cheng Z" first="Zong-Ming" last="Cheng">Zong-Ming Cheng</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21418570</idno><idno type="pmid">21418570</idno><idno type="doi">10.1186/1471-2105-12-79</idno><idno type="pmc">PMC3072343</idno><idno type="wicri:Area/Main/Corpus">002E81</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002E81</idno><idno type="wicri:Area/Main/Curation">002E81</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002E81</idno><idno type="wicri:Area/Main/Exploration">002E81</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">MicroSyn: a user friendly tool for detection of microsynteny in a gene family.</title><author><name sortKey="Cai, Bin" sort="Cai, Bin" uniqKey="Cai B" first="Bin" last="Cai">Bin Cai</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University</wicri:regionArea><wicri:noRegion>Nanjing Agricultural University</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name></author><author><name sortKey="Cheng, Zong Ming" sort="Cheng, Zong Ming" uniqKey="Cheng Z" first="Zong-Ming" last="Cheng">Zong-Ming Cheng</name></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genomics (methods)</term><term>MicroRNAs (genetics)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plants (classification)</term><term>Plants (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Software (MeSH)</term><term>Synteny (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Génomique (méthodes)</term><term>Logiciel (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Plantes (classification)</term><term>Plantes (génétique)</term><term>Synténie (génétique)</term><term>microARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plants</term><term>Synteny</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Plantes</term><term>Synténie</term><term>microARN</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Génomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Logiciel</term><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: http://fcsb.njau.edu.cn/microsyn/.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in Populus trichocarpa were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">21418570</PMID><DateCompleted><Year>2012</Year><Month>01</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><PubDate><Year>2011</Year><Month>Mar</Month><Day>18</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>MicroSyn: a user friendly tool for detection of microsynteny in a gene family.</ArticleTitle><Pagination><MedlinePgn>79</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2105-12-79</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. 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Chine</li></country></list><tree><noCountry><name sortKey="Cheng, Zong Ming" sort="Cheng, Zong Ming" uniqKey="Cheng Z" first="Zong-Ming" last="Cheng">Zong-Ming Cheng</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Cai, Bin" sort="Cai, Bin" uniqKey="Cai B" first="Bin" last="Cai">Bin Cai</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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