Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment
Identifieur interne : 000273 ( Ncbi/Checkpoint ); précédent : 000272; suivant : 000274Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment
Auteurs : Dadabhai T. Singh [Singapour] ; Rahul Trehan [Singapour] ; Bertil Schmidt [Australie] ; Timo Bretschneider [Singapour]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2008.
Abstract
Preparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any new emerging subtypes. Comparative phyloinformatics can be used to monitor, analyze, and possibly predict the evolution of viruses. However, in order to utilize the full functionality of available analysis packages for large-scale phyloinformatics studies, a team of computer scientists, biostatisticians and virologists is needed – a requirement which cannot be fulfilled in many cases. Furthermore, the time complexities of many algorithms involved leads to prohibitive runtimes on sequential computer platforms. This has so far hindered the use of comparative phyloinformatics as a commonly applied tool in this area.
In this paper the graphical-oriented workflow design system called
The current study demonstrates the efficiency and utility of workflow systems providing a biologist friendly approach to complex biological dataset analysis using high performance computing. In particular, the utility of the platform Quascade for deploying distributed and parallelized versions of a variety of computationally intensive phylogenetic algorithms has been shown. Secondly, the analysis of the utilized H5N1 neuraminidase datasets at macro and micro levels has clearly indicated a pattern of spatial clustering of the H5N1 viral isolates based on geographical distribution rather than temporal or host range based clustering.
The online version of this article (doi:10.1186/1471-2105-9-S1-S23) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2105-9-S1-S23
PubMed: 18315855
PubMed Central: 2259424
Affiliations:
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Singh</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Genvea Biosciences, 53 Craig Road, #04-01, 089691 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Genvea Biosciences, 53 Craig Road, #04-01</wicri:regionArea><wicri:noRegion>#04-01</wicri:noRegion></affiliation></author><author><name sortKey="Trehan, Rahul" sort="Trehan, Rahul" uniqKey="Trehan R" first="Rahul" last="Trehan">Rahul Trehan</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.59025.3b</institution-id><institution-id institution-id-type="ISNI">0000000122240361</institution-id><institution>Nanyang Technological University,</institution></institution-wrap>Nanyang Avenue N4-02a-32, 639798 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Nanyang Avenue N4-02a-32</wicri:regionArea></affiliation></author><author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name><affiliation wicri:level="1"><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="GRID">grid.1008.9</institution-id><institution-id institution-id-type="ISNI">000000012179088X</institution-id><institution>NICTA VRL,</institution><institution>University of Melbourne,</institution></institution-wrap>Parkville, 3010 Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Parkville</wicri:regionArea></affiliation></author><author><name sortKey="Bretschneider, Timo" sort="Bretschneider, Timo" uniqKey="Bretschneider T" first="Timo" last="Bretschneider">Timo Bretschneider</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.59025.3b</institution-id><institution-id institution-id-type="ISNI">0000000122240361</institution-id><institution>Nanyang Technological University,</institution></institution-wrap>Nanyang Avenue N4-02a-32, 639798 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Nanyang Avenue N4-02a-32</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Preparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any new emerging subtypes. Comparative phyloinformatics can be used to monitor, analyze, and possibly predict the evolution of viruses. However, in order to utilize the full functionality of available analysis packages for large-scale phyloinformatics studies, a team of computer scientists, biostatisticians and virologists is needed – a requirement which cannot be fulfilled in many cases. Furthermore, the time complexities of many algorithms involved leads to prohibitive runtimes on sequential computer platforms. This has so far hindered the use of comparative phyloinformatics as a commonly applied tool in this area.</p></sec><sec><title>Results</title><p>In this paper the graphical-oriented workflow design system called <italic>Quascade</italic> and its efficient usage for comparative phyloinformatics are presented. In particular, we focus on how this task can be effectively performed in a distributed computing environment. As a proof of concept, the designed workflows are used for the phylogenetic analysis of neuraminidase of H5N1 isolates (micro level) and influenza viruses (macro level). The results of this paper are hence twofold. Firstly, this paper demonstrates the usefulness of a graphical user interface system to design and execute complex distributed workflows for large-scale phyloinformatics studies of virus genes. Secondly, the analysis of neuraminidase on different levels of complexity provides valuable insights of this virus's tendency for geographical based clustering in the phylogenetic tree and also shows the importance of glycan sites in its molecular evolution.</p></sec><sec><title>Conclusion</title><p>The current study demonstrates the efficiency and utility of workflow systems providing a biologist friendly approach to complex biological dataset analysis using high performance computing. In particular, the utility of the platform Quascade for deploying distributed and parallelized versions of a variety of computationally intensive phylogenetic algorithms has been shown. Secondly, the analysis of the utilized H5N1 neuraminidase datasets at macro and micro levels has clearly indicated a pattern of spatial clustering of the H5N1 viral isolates based on geographical distribution rather than temporal or host range based clustering.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2105-9-S1-S23) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zambon, Mc" uniqKey="Zambon M">MC Zambon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Subbarao, K" uniqKey="Subbarao K">K Subbarao</name></author><author><name sortKey="Shaw, Mw" uniqKey="Shaw M">MW Shaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hatta, M" uniqKey="Hatta M">M Hatta</name></author><author><name sortKey="Kawaoka, Y" 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Romano</name></author><author><name sortKey="Bartocci, E" uniqKey="Bartocci E">E Bartocci</name></author><author><name sortKey="Bertolini, G" uniqKey="Bertolini G">G Bertolini</name></author><author><name sortKey="De Paoli, F" uniqKey="De Paoli F">F De Paoli</name></author><author><name sortKey="Marra, D" uniqKey="Marra D">D Marra</name></author><author><name sortKey="Mauri, G" uniqKey="Mauri G">G Mauri</name></author><author><name sortKey="Merelli, E" uniqKey="Merelli E">E Merelli</name></author><author><name sortKey="Milanesi, L" uniqKey="Milanesi L">L Milanesi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bartocci, E" uniqKey="Bartocci E">E Bartocci</name></author><author><name sortKey="Corradini, F" uniqKey="Corradini F">F Corradini</name></author><author><name sortKey="Merelli, E" uniqKey="Merelli E">E Merelli</name></author><author><name sortKey="Scortichini, L" uniqKey="Scortichini L">L Scortichini</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Singh, Dt" uniqKey="Singh D">DT Singh</name></author><author><name sortKey="Trehan, R" uniqKey="Trehan R">R Trehan</name></author><author><name sortKey="Ray, P" uniqKey="Ray P">P Ray</name></author><author><name sortKey="Schmidt, B" uniqKey="Schmidt B">B Schmidt</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Singapour</li></country></list><tree><country name="Singapour"><noRegion><name sortKey="Singh, Dadabhai T" sort="Singh, Dadabhai T" uniqKey="Singh D" first="Dadabhai T" last="Singh">Dadabhai T. Singh</name></noRegion><name sortKey="Bretschneider, Timo" sort="Bretschneider, Timo" uniqKey="Bretschneider T" first="Timo" last="Bretschneider">Timo Bretschneider</name><name sortKey="Trehan, Rahul" sort="Trehan, Rahul" uniqKey="Trehan R" first="Rahul" last="Trehan">Rahul Trehan</name></country><country name="Australie"><noRegion><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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