IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.
Identifieur interne : 002288 ( PubMed/Corpus ); précédent : 002287; suivant : 002289IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.
Auteurs : Giuseppe D'Auria ; Ravindra Pushker ; Francisco Rodriguez-ValeraSource :
- Bioinformatics (Oxford, England) [ 1367-4803 ] ; 2006.
English descriptors
- KwdEn :
- Algorithms, Conserved Sequence, DNA, Ribosomal Spacer (genetics), Databases, Genetic, Expressed Sequence Tags, Phylogeny, RNA, Bacterial (genetics), RNA, Ribosomal, 16S (classification), RNA, Ribosomal, 16S (genetics), RNA, Ribosomal, 23S (classification), RNA, Ribosomal, 23S (genetics), Sequence Alignment (methods), Sequence Analysis, RNA (methods), Sequence Homology, Nucleic Acid, Software, Species Specificity, Transcription, Genetic (genetics).
- MESH :
- chemical , classification : RNA, Ribosomal, 16S, RNA, Ribosomal, 23S.
- chemical , genetics : DNA, Ribosomal Spacer, RNA, Bacterial, RNA, Ribosomal, 16S, RNA, Ribosomal, 23S.
- genetics : Transcription, Genetic.
- methods : Sequence Alignment, Sequence Analysis, RNA.
- Algorithms, Conserved Sequence, Databases, Genetic, Expressed Sequence Tags, Phylogeny, Sequence Homology, Nucleic Acid, Software, Species Specificity.
Abstract
Lately the use of 16S-23S Intergenic Transcribed Spacer (ITS) sequences for bacterial typing purposes has increased. The presence of conserved regions like tRNA genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare.
DOI: 10.1093/bioinformatics/btk033
PubMed: 16403794
Links to Exploration step
pubmed:16403794Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.</title><author><name sortKey="D Auria, Giuseppe" sort="D Auria, Giuseppe" uniqKey="D Auria G" first="Giuseppe" last="D'Auria">Giuseppe D'Auria</name><affiliation><nlm:affiliation>Evolutionary Genomics Group and Division de Microbiologia, Universidad Miguel Hernandez Campus de San Juan, 03550 San Juan de Alicante, Spain. gdauria@umh.es</nlm:affiliation></affiliation></author><author><name sortKey="Pushker, Ravindra" sort="Pushker, Ravindra" uniqKey="Pushker R" first="Ravindra" last="Pushker">Ravindra Pushker</name></author><author><name sortKey="Rodriguez Valera, Francisco" sort="Rodriguez Valera, Francisco" uniqKey="Rodriguez Valera F" first="Francisco" last="Rodriguez-Valera">Francisco Rodriguez-Valera</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16403794</idno><idno type="pmid">16403794</idno><idno type="doi">10.1093/bioinformatics/btk033</idno><idno type="wicri:Area/PubMed/Corpus">002288</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002288</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.</title><author><name sortKey="D Auria, Giuseppe" sort="D Auria, Giuseppe" uniqKey="D Auria G" first="Giuseppe" last="D'Auria">Giuseppe D'Auria</name><affiliation><nlm:affiliation>Evolutionary Genomics Group and Division de Microbiologia, Universidad Miguel Hernandez Campus de San Juan, 03550 San Juan de Alicante, Spain. gdauria@umh.es</nlm:affiliation></affiliation></author><author><name sortKey="Pushker, Ravindra" sort="Pushker, Ravindra" uniqKey="Pushker R" first="Ravindra" last="Pushker">Ravindra Pushker</name></author><author><name sortKey="Rodriguez Valera, Francisco" sort="Rodriguez Valera, Francisco" uniqKey="Rodriguez Valera F" first="Francisco" last="Rodriguez-Valera">Francisco Rodriguez-Valera</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="ISSN">1367-4803</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Conserved Sequence</term><term>DNA, Ribosomal Spacer (genetics)</term><term>Databases, Genetic</term><term>Expressed Sequence Tags</term><term>Phylogeny</term><term>RNA, Bacterial (genetics)</term><term>RNA, Ribosomal, 16S (classification)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>RNA, Ribosomal, 23S (classification)</term><term>RNA, Ribosomal, 23S (genetics)</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, RNA (methods)</term><term>Sequence Homology, Nucleic Acid</term><term>Software</term><term>Species Specificity</term><term>Transcription, Genetic (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>RNA, Ribosomal, 16S</term><term>RNA, Ribosomal, 23S</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Ribosomal Spacer</term><term>RNA, Bacterial</term><term>RNA, Ribosomal, 16S</term><term>RNA, Ribosomal, 23S</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Alignment</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Conserved Sequence</term><term>Databases, Genetic</term><term>Expressed Sequence Tags</term><term>Phylogeny</term><term>Sequence Homology, Nucleic Acid</term><term>Software</term><term>Species Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Lately the use of 16S-23S Intergenic Transcribed Spacer (ITS) sequences for bacterial typing purposes has increased. The presence of conserved regions like tRNA genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16403794</PMID><DateCompleted><Year>2006</Year><Month>04</Month><Day>18</Day></DateCompleted><DateRevised><Year>2006</Year><Month>11</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1367-4803</ISSN><JournalIssue CitedMedium="Print"><Volume>22</Volume><Issue>5</Issue><PubDate><Year>2006</Year><Month>Mar</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.</ArticleTitle><Pagination><MedlinePgn>527-31</MedlinePgn></Pagination><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Lately the use of 16S-23S Intergenic Transcribed Spacer (ITS) sequences for bacterial typing purposes has increased. The presence of conserved regions like tRNA genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A software to study ITSs by a Word Count based System (IWoCS) is proposed. A large dataset of ITS was created (comprising 7355 sequences). A database indicating all the occurrences of possible n-mers (tags), describing each ITS sequence, was created (with n going from 5 to 13) including 32 061 819 entries. The database allows to analyze ITS sequences submitted by users using a web-based interface. The abundance in the database of each n-mer is given in a one-base sliding frame. A dominance plot reflects how common the tags are within different taxonomic levels. The obtained profile identifies highly repeated tags as evolutionarily conserved regions (like tRNA or boxes) or low frequency tags as regions specifically associated to taxonomic groups. The study of the dominance and abundance profiles combined with the taxonomy reports provides a novel tool for the use of the ITS in bacteria typing and identification.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">The database is freely accessible at http://egg.umh.es/iwocs/.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>D'Auria</LastName><ForeName>Giuseppe</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Evolutionary Genomics Group and Division de Microbiologia, Universidad Miguel Hernandez Campus de San Juan, 03550 San Juan de Alicante, Spain. gdauria@umh.es</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pushker</LastName><ForeName>Ravindra</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Rodriguez-Valera</LastName><ForeName>Francisco</ForeName><Initials>F</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>01</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021903">DNA, Ribosomal Spacer</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012329">RNA, Bacterial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012338">RNA, Ribosomal, 23S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021903" MajorTopicYN="N">DNA, Ribosomal Spacer</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012329" MajorTopicYN="N">RNA, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012338" MajorTopicYN="N">RNA, Ribosomal, 23S</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012689" MajorTopicYN="N">Sequence Homology, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>1</Month><Day>13</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>4</Month><Day>19</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>1</Month><Day>13</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16403794</ArticleId><ArticleId IdType="pii">btk033</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btk033</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002288 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 002288 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:16403794
|texte= IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:16403794" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |