Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment

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Metadaten:
Abstract
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats: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.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In this paper the graphical-oriented workflow design system called<jats:italic>Quascade</jats: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.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats: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.</jats:p></jats:sec>
Autoren
DOI
10.1186/1471-2105-9-s1-s23
eISSN
1471-2105
Ausgabe der Veröffentlichung
S1
Zeitschrift
BMC Bioinformatics
Sprache
en
Artikelnummer
S23
Online publication date
2008
Datum der Veröffentlichung
2008
Status
Published
Herausgeber
Springer Science and Business Media LLC
Herausgeber URL
http://dx.doi.org/10.1186/1471-2105-9-s1-s23
Datum der Datenerfassung
2023
Titel
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment
Ausgabe der Zeitschrift
9

Datenquelle: Crossref

Andere Metadatenquellen:
Abstract
<h4>Background</h4>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.<h4>Results</h4>In this paper the graphical-oriented workflow design system called Quascade 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.<h4>Conclusion</h4>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.
Addresses
  • Genvea Biosciences, 53 Craig Road, #04-01, Singapore 089691. dtsingh@genvea.com
Autoren
DOI
10.1186/1471-2105-9-s1-s23
eISSN
1471-2105
Externe Identifier
  • PubMed Identifier: 18315855
  • PubMed Central ID: PMC2259424
Open access
true
ISSN
1471-2105
Zeitschrift
BMC bioinformatics
Schlüsselwörter
  • Neuraminidase
  • Viral Proteins
  • DNA Mutational Analysis
  • Computational Biology
  • Evolution, Molecular
  • Phylogeny
  • Computing Methodologies
  • Computer Communication Networks
  • Influenza A Virus, H5N1 Subtype
Sprache
eng
Medium
Print
Open access status
Open Access
Paginierung
S23
Datum der Veröffentlichung
2008
Status
Published
Datum der Datenerfassung
2008
Titel
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.
Sub types
  • Journal Article
  • case-report
Ausgabe der Zeitschrift
9 Suppl 1

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https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-S1-S23 https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18315855/pdf/?tool=EBI http://www.biomedcentral.com/content/pdf/1471-2105-9_suppl_1-S23.pdf https://europepmc.org/articles/PMC2259424?pdf=render

Datenquelle: Europe PubMed Central

Abstract
BACKGROUND: 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. RESULTS: In this paper the graphical-oriented workflow design system called Quascade 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. CONCLUSION: 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.
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/18315855
DOI
10.1186/1471-2105-9-S1-S23
eISSN
1471-2105
Externe Identifier
  • PubMed Central ID: PMC2259424
Ausgabe der Veröffentlichung
Suppl 1
Zeitschrift
BMC Bioinformatics
Schlüsselwörter
  • Computational Biology
  • Computer Communication Networks
  • Computing Methodologies
  • DNA Mutational Analysis
  • Evolution, Molecular
  • Influenza A Virus, H5N1 Subtype
  • Neuraminidase
  • Phylogeny
  • Viral Proteins
Sprache
eng
Country
England
Paginierung
S23
PII
1471-2105-9-S1-S23
Datum der Veröffentlichung
2008
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2008
Titel
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
9 Suppl 1

Datenquelle: PubMed

Autoren
Zeitschrift
BMC Bioinform.
Artikelnummer
S-1
Datum der Veröffentlichung
2008
Titel
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.
Ausgabe der Zeitschrift
9

Datenquelle: DBLP

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