MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
Identifieur interne : 000320 ( Main/Exploration ); précédent : 000319; suivant : 000321MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
Auteurs : Kishori M. Konwar [Canada] ; Niels W. Hanson ; Antoine P. Pagé [Canada] ; Steven J. Hallam [Canada]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2013.
Abstract
A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information. The dominant paradigm in metabolic reconstruction is to assign functional annotations using BLAST. Functional annotations are then projected onto symbolic representations of metabolism in the form of KEGG pathways or SEED subsystems.
Here we present MetaPathways, an open source pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools. The pipeline accepts assembled or unassembled nucleotide sequences, performs quality assessment and control, predicts and annotates noncoding genes and open reading frames, and produces inputs to PathoLogic. In addition to constructing ePGDBs, MetaPathways uses MLTreeMap to build phylogenetic trees for selected taxonomic anchor and functional gene markers, converts General Feature Format (GFF) files into concatenated GenBank files for ePGDB construction based on third-party annotations, and generates useful file formats including Sequin files for direct GenBank submission and gene feature tables summarizing annotations, MLTreeMap trees, and ePGDB pathway coverage summaries for statistical comparisons.
MetaPathways provides users with a modular annotation and analysis pipeline for predicting metabolic interaction networks from environmental sequence information using an alternative to KEGG pathways and SEED subsystems mapping. It is extensible to genomic and transcriptomic datasets from a wide range of sequencing platforms, and generates useful data products for microbial community structure and function analysis. The MetaPathways software package, installation instructions, and example data can be obtained from
Url:
DOI: 10.1186/1471-2105-14-202
PubMed: 23800136
PubMed Central: 3695837
Affiliations:
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Hanson</name><affiliation><nlm:aff id="I2">Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Page, Antoine P" sort="Page, Antoine P" uniqKey="Page A" first="Antoine P" last="Pagé">Antoine P. Pagé</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3</wicri:regionArea><wicri:noRegion>BC V6T1Z3</wicri:noRegion></affiliation></author><author><name sortKey="Hallam, Steven J" sort="Hallam, Steven J" uniqKey="Hallam S" first="Steven J" last="Hallam">Steven J. 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Konwar</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3</wicri:regionArea><wicri:noRegion>BC V6T1Z3</wicri:noRegion></affiliation></author><author><name sortKey="Hanson, Niels W" sort="Hanson, Niels W" uniqKey="Hanson N" first="Niels W" last="Hanson">Niels W. Hanson</name><affiliation><nlm:aff id="I2">Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Page, Antoine P" sort="Page, Antoine P" uniqKey="Page A" first="Antoine P" last="Pagé">Antoine P. Pagé</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3</wicri:regionArea><wicri:noRegion>BC V6T1Z3</wicri:noRegion></affiliation></author><author><name sortKey="Hallam, Steven J" sort="Hallam, Steven J" uniqKey="Hallam S" first="Steven J" last="Hallam">Steven J. Hallam</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3</wicri:regionArea><wicri:noRegion>BC V6T1Z3</wicri:noRegion></affiliation><affiliation><nlm:aff id="I2">Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information. The dominant paradigm in metabolic reconstruction is to assign functional annotations using BLAST. Functional annotations are then projected onto symbolic representations of metabolism in the form of KEGG pathways or SEED subsystems.</p></sec><sec><title>Results</title><p>Here we present MetaPathways, an open source pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools. The pipeline accepts assembled or unassembled nucleotide sequences, performs quality assessment and control, predicts and annotates noncoding genes and open reading frames, and produces inputs to PathoLogic. In addition to constructing ePGDBs, MetaPathways uses MLTreeMap to build phylogenetic trees for selected taxonomic anchor and functional gene markers, converts General Feature Format (GFF) files into concatenated GenBank files for ePGDB construction based on third-party annotations, and generates useful file formats including Sequin files for direct GenBank submission and gene feature tables summarizing annotations, MLTreeMap trees, and ePGDB pathway coverage summaries for statistical comparisons.</p></sec><sec><title>Conclusions</title><p>MetaPathways provides users with a modular annotation and analysis pipeline for predicting metabolic interaction networks from environmental sequence information using an alternative to KEGG pathways and SEED subsystems mapping. It is extensible to genomic and transcriptomic datasets from a wide range of sequencing platforms, and generates useful data products for microbial community structure and function analysis. The MetaPathways software package, installation instructions, and example data can be obtained from <ext-link ext-link-type="uri" xlink:href="http://hallam.microbiology.ubc.ca/MetaPathways">http://hallam.microbiology.ubc.ca/MetaPathways</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wright, Jj" uniqKey="Wright J">JJ Wright</name></author><author><name sortKey="Konwar, Km" uniqKey="Konwar K">KM Konwar</name></author><author><name sortKey="Hallam, Sj" uniqKey="Hallam S">SJ Hallam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Delong, Ef" uniqKey="Delong E">EF Delong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Falkowski, Pg" uniqKey="Falkowski P">PG Falkowski</name></author><author><name sortKey="Fenchel, T" uniqKey="Fenchel T">T Fenchel</name></author><author><name sortKey="Delong, Ef" uniqKey="Delong E">EF 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Brendel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yooseph, S" uniqKey="Yooseph S">S Yooseph</name></author><author><name sortKey="Sutton, G" uniqKey="Sutton G">G Sutton</name></author><author><name sortKey="Rusch, Db" uniqKey="Rusch D">DB Rusch</name></author><author><name sortKey="Halpern, Al" uniqKey="Halpern A">AL Halpern</name></author><author><name sortKey="Williamson, Sj" uniqKey="Williamson S">SJ Williamson</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K Remington</name></author><author><name sortKey="Eisen, Ja" uniqKey="Eisen J">JA Eisen</name></author><author><name sortKey="Heidelberg, Kb" uniqKey="Heidelberg K">KB Heidelberg</name></author><author><name sortKey="Manning, G" uniqKey="Manning G">G Manning</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kalyanaraman, A" uniqKey="Kalyanaraman A">A Kalyanaraman</name></author><author><name sortKey="Cannon, Wr" uniqKey="Cannon W">WR Cannon</name></author><author><name sortKey="Latt, B" uniqKey="Latt B">B Latt</name></author><author><name sortKey="Baxter, Dj" uniqKey="Baxter D">DJ Baxter</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li></country></list><tree><noCountry><name sortKey="Hanson, Niels W" sort="Hanson, Niels W" uniqKey="Hanson N" first="Niels W" last="Hanson">Niels W. Hanson</name></noCountry><country name="Canada"><noRegion><name sortKey="Konwar, Kishori M" sort="Konwar, Kishori M" uniqKey="Konwar K" first="Kishori M" last="Konwar">Kishori M. Konwar</name></noRegion><name sortKey="Hallam, Steven J" sort="Hallam, Steven J" uniqKey="Hallam S" first="Steven J" last="Hallam">Steven J. Hallam</name><name sortKey="Page, Antoine P" sort="Page, Antoine P" uniqKey="Page A" first="Antoine P" last="Pagé">Antoine P. Pagé</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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