BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences
Identifieur interne : 000744 ( Main/Exploration ); précédent : 000743; suivant : 000745BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences
Auteurs : Damiano Piovesan ; Pier Luigi Martelli ; Piero Fariselli ; Andrea Zauli [Italie] ; Ivan Rossi [Italie] ; Rita CasadioSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2011.
Abstract
We introduce BAR-PLUS (BAR+), a web server for functional and structural annotation of protein sequences. BAR+ is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13 495 736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10 858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence–structural target alignments computed from the correspondent Cluster-HMM. BAR+ in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR+ is available at
Url:
DOI: 10.1093/nar/gkr292
PubMed: 21622657
PubMed Central: 3125743
Affiliations:
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Le document en format XML
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first="Andrea" last="Zauli">Andrea Zauli</name><affiliation wicri:level="1"><nlm:aff id="AFF1">BioDec srl, Bologna, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>BioDec srl, Bologna</wicri:regionArea><wicri:noRegion>Bologna</wicri:noRegion></affiliation></author><author><name sortKey="Rossi, Ivan" sort="Rossi, Ivan" uniqKey="Rossi I" first="Ivan" last="Rossi">Ivan Rossi</name><affiliation wicri:level="1"><nlm:aff id="AFF1">BioDec srl, Bologna, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>BioDec srl, Bologna</wicri:regionArea><wicri:noRegion>Bologna</wicri:noRegion></affiliation></author><author><name sortKey="Casadio, Rita" sort="Casadio, Rita" uniqKey="Casadio R" first="Rita" last="Casadio">Rita Casadio</name><affiliation><nlm:aff id="AFF1">Department of Biology, Bologna Biocomputing Group, Bologna Computational Biology Network,</nlm:aff><wicri:noCountry code="subfield">Bologna Computational Biology Network</wicri:noCountry></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We introduce BAR-PLUS (BAR<sup>+</sup>), a web server for functional and structural annotation of protein sequences. BAR<sup>+</sup> is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13 495 736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10 858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence–structural target alignments computed from the correspondent Cluster-HMM. BAR<sup>+</sup> in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR<sup>+</sup> is available at <ext-link ext-link-type="uri" xlink:href="http://bar.biocomp.unibo.it/bar2.0">http://bar.biocomp.unibo.it/bar2.0</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Krause, A" uniqKey="Krause A">A Krause</name></author><author><name sortKey="Stoye, J" uniqKey="Stoye J">J Stoye</name></author><author><name sortKey="Vingron, M" uniqKey="Vingron M">M Vingron</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heger, A" uniqKey="Heger A">A Heger</name></author><author><name sortKey="Holm, L" uniqKey="Holm L">L Holm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Ch" uniqKey="Wu C">CH Wu</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Nikolskaya, A" uniqKey="Nikolskaya A">A Nikolskaya</name></author><author><name sortKey="Hu, Z" uniqKey="Hu Z">Z 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uniqKey="Eddy S">SR Eddy</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Italie</li></country></list><tree><noCountry><name sortKey="Casadio, Rita" sort="Casadio, Rita" uniqKey="Casadio R" first="Rita" last="Casadio">Rita Casadio</name><name sortKey="Fariselli, Piero" sort="Fariselli, Piero" uniqKey="Fariselli P" first="Piero" last="Fariselli">Piero Fariselli</name><name sortKey="Luigi Martelli, Pier" sort="Luigi Martelli, Pier" uniqKey="Luigi Martelli P" first="Pier" last="Luigi Martelli">Pier Luigi Martelli</name><name sortKey="Piovesan, Damiano" sort="Piovesan, Damiano" uniqKey="Piovesan D" first="Damiano" last="Piovesan">Damiano Piovesan</name></noCountry><country name="Italie"><noRegion><name sortKey="Zauli, Andrea" sort="Zauli, Andrea" uniqKey="Zauli A" first="Andrea" last="Zauli">Andrea Zauli</name></noRegion><name sortKey="Rossi, Ivan" sort="Rossi, Ivan" uniqKey="Rossi I" first="Ivan" last="Rossi">Ivan 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