MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
Identifieur interne : 000274 ( Pmc/Curation ); précédent : 000273; suivant : 000275MetaPathways: 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
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Niels W. Hanson<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>
<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>
Le document en format XML
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<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>
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</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 Delong</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kunin, V" uniqKey="Kunin V">V Kunin</name>
</author>
<author><name sortKey="Copeland, A" uniqKey="Copeland A">A Copeland</name>
</author>
<author><name sortKey="Lapidus, A" uniqKey="Lapidus A">A Lapidus</name>
</author>
<author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</name>
</author>
<author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</name>
</author>
<author><name sortKey="Ivanova, N" uniqKey="Ivanova N">N Ivanova</name>
</author>
<author><name sortKey="Barry, K" uniqKey="Barry K">K Barry</name>
</author>
<author><name sortKey="Shapiro, H" uniqKey="Shapiro H">H Shapiro</name>
</author>
<author><name sortKey="Goltsman, E" uniqKey="Goltsman E">E Goltsman</name>
</author>
<author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</name>
</author>
<author><name sortKey="Rigoutsos, I" uniqKey="Rigoutsos I">I Rigoutsos</name>
</author>
<author><name sortKey="Salamov, A" uniqKey="Salamov A">A Salamov</name>
</author>
<author><name sortKey="Korzeniewski, F" uniqKey="Korzeniewski F">F Korzeniewski</name>
</author>
<author><name sortKey="Land, M" uniqKey="Land M">M Land</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wooley, Jc" uniqKey="Wooley J">JC Wooley</name>
</author>
<author><name sortKey="Godzik, A" uniqKey="Godzik A">A Godzik</name>
</author>
<author><name sortKey="Friedberg, I" uniqKey="Friedberg I">I Friedberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name>
</author>
<author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name>
</author>
<author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name>
</author>
<author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name>
</author>
<author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kanehisa, M" uniqKey="Kanehisa M">M Kanehisa</name>
</author>
<author><name sortKey="Goto, S" uniqKey="Goto S">S Goto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Okuda, S" uniqKey="Okuda S">S Okuda</name>
</author>
<author><name sortKey="Yamada, T" uniqKey="Yamada T">T Yamada</name>
</author>
<author><name sortKey="Hamajima, M" uniqKey="Hamajima M">M Hamajima</name>
</author>
<author><name sortKey="Itoh, M" uniqKey="Itoh M">M Itoh</name>
</author>
<author><name sortKey="Katayama, T" uniqKey="Katayama T">T Katayama</name>
</author>
<author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name>
</author>
<author><name sortKey="Goto, S" uniqKey="Goto S">S Goto</name>
</author>
<author><name sortKey="Kanehisa, M" uniqKey="Kanehisa M">M Kanehisa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Claudel Renard, C" uniqKey="Claudel Renard C">C Claudel Renard</name>
</author>
<author><name sortKey="Chevalet, C" uniqKey="Chevalet C">C Chevalet</name>
</author>
<author><name sortKey="Faraut, T" uniqKey="Faraut T">T Faraut</name>
</author>
<author><name sortKey="Kahn, D" uniqKey="Kahn D">D Kahn</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R Overbeek</name>
</author>
<author><name sortKey="Begley, T" uniqKey="Begley T">T Begley</name>
</author>
<author><name sortKey="Butler, Rm" uniqKey="Butler R">RM Butler</name>
</author>
<author><name sortKey="Choudhuri, Jv" uniqKey="Choudhuri J">JV Choudhuri</name>
</author>
<author><name sortKey="Chuang, H Y" uniqKey="Chuang H">H-Y Chuang</name>
</author>
<author><name sortKey="Cohoon, M" uniqKey="Cohoon M">M Cohoon</name>
</author>
<author><name sortKey="De Crecy Lagard, V" uniqKey="De Crecy Lagard V">V de Crécy-Lagard</name>
</author>
<author><name sortKey="Diaz, N" uniqKey="Diaz N">N Diaz</name>
</author>
<author><name sortKey="Disz, T" uniqKey="Disz T">T Disz</name>
</author>
<author><name sortKey="Edwards, R" uniqKey="Edwards R">R Edwards</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name>
</author>
<author><name sortKey="Ivanova, Nn" uniqKey="Ivanova N">NN Ivanova</name>
</author>
<author><name sortKey="Szeto, E" uniqKey="Szeto E">E Szeto</name>
</author>
<author><name sortKey="Palaniappan, K" uniqKey="Palaniappan K">K Palaniappan</name>
</author>
<author><name sortKey="Chu, K" uniqKey="Chu K">K Chu</name>
</author>
<author><name sortKey="Dalevi, D" uniqKey="Dalevi D">D Dalevi</name>
</author>
<author><name sortKey="Chen, I Ma" uniqKey="Chen I">I-MA Chen</name>
</author>
<author><name sortKey="Grechkin, Y" uniqKey="Grechkin Y">Y Grechkin</name>
</author>
<author><name sortKey="Dubchak, I" uniqKey="Dubchak I">I Dubchak</name>
</author>
<author><name sortKey="Anderson, I" uniqKey="Anderson I">I Anderson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name>
</author>
<author><name sortKey="Chen, I Ma" uniqKey="Chen I">I-MA Chen</name>
</author>
<author><name sortKey="Chu, K" uniqKey="Chu K">K Chu</name>
</author>
<author><name sortKey="Szeto, E" uniqKey="Szeto E">E Szeto</name>
</author>
<author><name sortKey="Palaniappan, K" uniqKey="Palaniappan K">K Palaniappan</name>
</author>
<author><name sortKey="Grechkin, Y" uniqKey="Grechkin Y">Y Grechkin</name>
</author>
<author><name sortKey="Ratner, A" uniqKey="Ratner A">A Ratner</name>
</author>
<author><name sortKey="Jacob, B" uniqKey="Jacob B">B Jacob</name>
</author>
<author><name sortKey="Pati, A" uniqKey="Pati A">A Pati</name>
</author>
<author><name sortKey="Huntemann, M" uniqKey="Huntemann M">M Huntemann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Seshadri, R" uniqKey="Seshadri R">R Seshadri</name>
</author>
<author><name sortKey="Kravitz, Sa" uniqKey="Kravitz S">SA Kravitz</name>
</author>
<author><name sortKey="Smarr, L" uniqKey="Smarr L">L Smarr</name>
</author>
<author><name sortKey="Gilna, P" uniqKey="Gilna P">P Gilna</name>
</author>
<author><name sortKey="Frazier, M" uniqKey="Frazier M">M Frazier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Paarmann, D" uniqKey="Paarmann D">D Paarmann</name>
</author>
<author><name sortKey="D Souza, M" uniqKey="D Souza M">M D'Souza</name>
</author>
<author><name sortKey="Olson, R" uniqKey="Olson R">R Olson</name>
</author>
<author><name sortKey="Glass, Em" uniqKey="Glass E">EM Glass</name>
</author>
<author><name sortKey="Kubal, M" uniqKey="Kubal M">M Kubal</name>
</author>
<author><name sortKey="Paczian, T" uniqKey="Paczian T">T Paczian</name>
</author>
<author><name sortKey="Rodriguez, A" uniqKey="Rodriguez A">A Rodriguez</name>
</author>
<author><name sortKey="Stevens, R" uniqKey="Stevens R">R Stevens</name>
</author>
<author><name sortKey="Wilke, A" uniqKey="Wilke A">A Wilke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aziz, Rk" uniqKey="Aziz R">RK Aziz</name>
</author>
<author><name sortKey="Bartels, D" uniqKey="Bartels D">D Bartels</name>
</author>
<author><name sortKey="Best, Aa" uniqKey="Best A">AA Best</name>
</author>
<author><name sortKey="Dejongh, M" uniqKey="Dejongh M">M DeJongh</name>
</author>
<author><name sortKey="Disz, T" uniqKey="Disz T">T Disz</name>
</author>
<author><name sortKey="Edwards, Ra" uniqKey="Edwards R">RA Edwards</name>
</author>
<author><name sortKey="Formsma, K" uniqKey="Formsma K">K Formsma</name>
</author>
<author><name sortKey="Gerdes, S" uniqKey="Gerdes S">S Gerdes</name>
</author>
<author><name sortKey="Glass, Em" uniqKey="Glass E">EM Glass</name>
</author>
<author><name sortKey="Kubal, M" uniqKey="Kubal M">M Kubal</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R Overbeek</name>
</author>
<author><name sortKey="Rodriguez, A" uniqKey="Rodriguez A">A Rodriguez</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
<author><name sortKey="Paley, S" uniqKey="Paley S">S Paley</name>
</author>
<author><name sortKey="Romero, P" uniqKey="Romero P">P Romero</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
<author><name sortKey="Paley, Sm" uniqKey="Paley S">SM Paley</name>
</author>
<author><name sortKey="Krummenacker, M" uniqKey="Krummenacker M">M Krummenacker</name>
</author>
<author><name sortKey="Latendresse, M" uniqKey="Latendresse M">M Latendresse</name>
</author>
<author><name sortKey="Dale, Jm" uniqKey="Dale J">JM Dale</name>
</author>
<author><name sortKey="Lee, Tj" uniqKey="Lee T">TJ Lee</name>
</author>
<author><name sortKey="Kaipa, P" uniqKey="Kaipa P">P Kaipa</name>
</author>
<author><name sortKey="Gilham, F" uniqKey="Gilham F">F Gilham</name>
</author>
<author><name sortKey="Spaulding, A" uniqKey="Spaulding A">A Spaulding</name>
</author>
<author><name sortKey="Popescu, L" uniqKey="Popescu L">L Popescu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
<author><name sortKey="Latendresse, M" uniqKey="Latendresse M">M Latendresse</name>
</author>
<author><name sortKey="Caspi, R" uniqKey="Caspi R">R Caspi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Latendresse, M" uniqKey="Latendresse M">M Latendresse</name>
</author>
<author><name sortKey="Krummenacker, M" uniqKey="Krummenacker M">M Krummenacker</name>
</author>
<author><name sortKey="Trupp, M" uniqKey="Trupp M">M Trupp</name>
</author>
<author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hucka, M" uniqKey="Hucka M">M Hucka</name>
</author>
<author><name sortKey="Finney, A" uniqKey="Finney A">A Finney</name>
</author>
<author><name sortKey="Sauro, Hm" uniqKey="Sauro H">HM Sauro</name>
</author>
<author><name sortKey="Bolouri, H" uniqKey="Bolouri H">H Bolouri</name>
</author>
<author><name sortKey="Doyle, Jc" uniqKey="Doyle J">JC Doyle</name>
</author>
<author><name sortKey="Kitano, H" uniqKey="Kitano H">H Kitano</name>
</author>
<author><name sortKey="Arkin, Ap" uniqKey="Arkin A">AP Arkin</name>
</author>
<author><name sortKey="Bornstein, Bj" uniqKey="Bornstein B">BJ Bornstein</name>
</author>
<author><name sortKey="Bray, D" uniqKey="Bray D">D Bray</name>
</author>
<author><name sortKey="Cornish Bowden, A" uniqKey="Cornish Bowden A">A Cornish-Bowden</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
<author><name sortKey="Riley, M" uniqKey="Riley M">M Riley</name>
</author>
<author><name sortKey="Saier, M" uniqKey="Saier M">M Saier</name>
</author>
<author><name sortKey="Paulsen, It" uniqKey="Paulsen I">IT Paulsen</name>
</author>
<author><name sortKey="Paley, Sm" uniqKey="Paley S">SM Paley</name>
</author>
<author><name sortKey="Pellegrini Toole, A" uniqKey="Pellegrini Toole A">A Pellegrini-Toole</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Caspi, R" uniqKey="Caspi R">R Caspi</name>
</author>
<author><name sortKey="Altman, T" uniqKey="Altman T">T Altman</name>
</author>
<author><name sortKey="Dreher, K" uniqKey="Dreher K">K Dreher</name>
</author>
<author><name sortKey="Fulcher, Ca" uniqKey="Fulcher C">CA Fulcher</name>
</author>
<author><name sortKey="Subhraveti, P" uniqKey="Subhraveti P">P Subhraveti</name>
</author>
<author><name sortKey="Keseler, Im" uniqKey="Keseler I">IM Keseler</name>
</author>
<author><name sortKey="Kothari, A" uniqKey="Kothari A">A Kothari</name>
</author>
<author><name sortKey="Krummenacker, M" uniqKey="Krummenacker M">M Krummenacker</name>
</author>
<author><name sortKey="Latendresse, M" uniqKey="Latendresse M">M Latendresse</name>
</author>
<author><name sortKey="Mueller, La" uniqKey="Mueller L">LA Mueller</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Latendresse, M" uniqKey="Latendresse M">M Latendresse</name>
</author>
<author><name sortKey="Paley, S" uniqKey="Paley S">S Paley</name>
</author>
<author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stark, M" uniqKey="Stark M">M Stark</name>
</author>
<author><name sortKey="Berger, Sa" uniqKey="Berger S">SA Berger</name>
</author>
<author><name sortKey="Stamatakis, A" uniqKey="Stamatakis A">A Stamatakis</name>
</author>
<author><name sortKey="Mering Von, C" uniqKey="Mering Von C">C Mering von</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hyatt, D" uniqKey="Hyatt D">D Hyatt</name>
</author>
<author><name sortKey="Chen, G L" uniqKey="Chen G">G-L Chen</name>
</author>
<author><name sortKey="Locascio, Pf" uniqKey="Locascio P">PF LoCascio</name>
</author>
<author><name sortKey="Land, Ml" uniqKey="Land M">ML Land</name>
</author>
<author><name sortKey="Larimer, Fw" uniqKey="Larimer F">FW Larimer</name>
</author>
<author><name sortKey="Hauser, Lj" uniqKey="Hauser L">LJ Hauser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tatusov, Rl" uniqKey="Tatusov R">RL Tatusov</name>
</author>
<author><name sortKey="Natale, Da" uniqKey="Natale D">DA Natale</name>
</author>
<author><name sortKey="Garkavtsev, Iv" uniqKey="Garkavtsev I">IV Garkavtsev</name>
</author>
<author><name sortKey="Tatusova, Ta" uniqKey="Tatusova T">TA Tatusova</name>
</author>
<author><name sortKey="Shankavaram, Ut" uniqKey="Shankavaram U">UT Shankavaram</name>
</author>
<author><name sortKey="Rao, Bs" uniqKey="Rao B">BS Rao</name>
</author>
<author><name sortKey="Kiryutin, B" uniqKey="Kiryutin B">B Kiryutin</name>
</author>
<author><name sortKey="Galperin, My" uniqKey="Galperin M">MY Galperin</name>
</author>
<author><name sortKey="Fedorova, Nd" uniqKey="Fedorova N">ND Fedorova</name>
</author>
<author><name sortKey="Koonin, Ev" uniqKey="Koonin E">EV Koonin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pruitt, Kd" uniqKey="Pruitt K">KD Pruitt</name>
</author>
<author><name sortKey="Maglott, Dr" uniqKey="Maglott D">DR Maglott</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kielbasa, Sm" uniqKey="Kielbasa S">SM Kiełbasa</name>
</author>
<author><name sortKey="Wan, R" uniqKey="Wan R">R Wan</name>
</author>
<author><name sortKey="Sato, K" uniqKey="Sato K">K Sato</name>
</author>
<author><name sortKey="Horton, P" uniqKey="Horton P">P Horton</name>
</author>
<author><name sortKey="Frith, Mc" uniqKey="Frith M">MC Frith</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rasko, Da" uniqKey="Rasko D">DA Rasko</name>
</author>
<author><name sortKey="Myers, Gsa" uniqKey="Myers G">GSA Myers</name>
</author>
<author><name sortKey="Ravel, J" uniqKey="Ravel J">J Ravel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rost, B" uniqKey="Rost B">B Rost</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gentzsch, W" uniqKey="Gentzsch W">W Gentzsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pruesse, E" uniqKey="Pruesse E">E Pruesse</name>
</author>
<author><name sortKey="Quast, C" uniqKey="Quast C">C Quast</name>
</author>
<author><name sortKey="Knittel, K" uniqKey="Knittel K">K Knittel</name>
</author>
<author><name sortKey="Fuchs, Bm" uniqKey="Fuchs B">BM Fuchs</name>
</author>
<author><name sortKey="Ludwig, W" uniqKey="Ludwig W">W Ludwig</name>
</author>
<author><name sortKey="Peplies, J" uniqKey="Peplies J">J Peplies</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glöckner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Desantis, Tz" uniqKey="Desantis T">TZ DeSantis</name>
</author>
<author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name>
</author>
<author><name sortKey="Larsen, N" uniqKey="Larsen N">N Larsen</name>
</author>
<author><name sortKey="Rojas, M" uniqKey="Rojas M">M Rojas</name>
</author>
<author><name sortKey="Brodie, El" uniqKey="Brodie E">EL Brodie</name>
</author>
<author><name sortKey="Keller, K" uniqKey="Keller K">K Keller</name>
</author>
<author><name sortKey="Huber, T" uniqKey="Huber T">T Huber</name>
</author>
<author><name sortKey="Dalevi, D" uniqKey="Dalevi D">D Dalevi</name>
</author>
<author><name sortKey="Hu, P" uniqKey="Hu P">P Hu</name>
</author>
<author><name sortKey="Andersen, Gl" uniqKey="Andersen G">GL Andersen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lowe, Tm" uniqKey="Lowe T">TM Lowe</name>
</author>
<author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
<author><name sortKey="Auch, Af" uniqKey="Auch A">AF Auch</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
<author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Latendresse, M" uniqKey="Latendresse M">M Latendresse</name>
</author>
<author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Paley, Sm" uniqKey="Paley S">SM Paley</name>
</author>
<author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Dale, Jm" uniqKey="Dale J">JM Dale</name>
</author>
<author><name sortKey="Popescu, L" uniqKey="Popescu L">L Popescu</name>
</author>
<author><name sortKey="Karp, Pd" uniqKey="Karp P">PD Karp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Richter, Dc" uniqKey="Richter D">DC Richter</name>
</author>
<author><name sortKey="Ott, F" uniqKey="Ott F">F Ott</name>
</author>
<author><name sortKey="Auch, Af" uniqKey="Auch A">AF Auch</name>
</author>
<author><name sortKey="Schmid, R" uniqKey="Schmid R">R Schmid</name>
</author>
<author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barton, Ad" uniqKey="Barton A">AD Barton</name>
</author>
<author><name sortKey="Dutkiewicz, S" uniqKey="Dutkiewicz S">S Dutkiewicz</name>
</author>
<author><name sortKey="Flierl, G" uniqKey="Flierl G">G Flierl</name>
</author>
<author><name sortKey="Bragg, J" uniqKey="Bragg J">J Bragg</name>
</author>
<author><name sortKey="Follows, Mj" uniqKey="Follows M">MJ Follows</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Follows, Mj" uniqKey="Follows M">MJ Follows</name>
</author>
<author><name sortKey="Dutkiewicz, S" uniqKey="Dutkiewicz S">S Dutkiewicz</name>
</author>
<author><name sortKey="Grant, S" uniqKey="Grant S">S Grant</name>
</author>
<author><name sortKey="Chisholm, Sw" uniqKey="Chisholm S">SW Chisholm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Larsen, Pe" uniqKey="Larsen P">PE Larsen</name>
</author>
<author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
<author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Larsen, Pe" uniqKey="Larsen P">PE Larsen</name>
</author>
<author><name sortKey="Collart, Fr" uniqKey="Collart F">FR Collart</name>
</author>
<author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
<author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Keegan, Kp" uniqKey="Keegan K">KP Keegan</name>
</author>
<author><name sortKey="Henry, Cs" uniqKey="Henry C">CS Henry</name>
</author>
<author><name sortKey="Mcgrath, J" uniqKey="Mcgrath J">J McGrath</name>
</author>
<author><name sortKey="Quinn, J" uniqKey="Quinn J">J Quinn</name>
</author>
<author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S Abubucker</name>
</author>
<author><name sortKey="Segata, N" uniqKey="Segata N">N Segata</name>
</author>
<author><name sortKey="Goll, J" uniqKey="Goll J">J Goll</name>
</author>
<author><name sortKey="Schubert, Am" uniqKey="Schubert A">AM Schubert</name>
</author>
<author><name sortKey="Izard, J" uniqKey="Izard J">J Izard</name>
</author>
<author><name sortKey="Cantarel, Bl" uniqKey="Cantarel B">BL Cantarel</name>
</author>
<author><name sortKey="Rodriguez Mueller, B" uniqKey="Rodriguez Mueller B">B Rodriguez-Mueller</name>
</author>
<author><name sortKey="Zucker, J" uniqKey="Zucker J">J Zucker</name>
</author>
<author><name sortKey="Thiagarajan, M" uniqKey="Thiagarajan M">M Thiagarajan</name>
</author>
<author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B Henrissat</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ye, Y" uniqKey="Ye Y">Y Ye</name>
</author>
<author><name sortKey="Doak, Tg" uniqKey="Doak T">TG Doak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Goll, J" uniqKey="Goll J">J Goll</name>
</author>
<author><name sortKey="Thiagarajan, M" uniqKey="Thiagarajan M">M Thiagarajan</name>
</author>
<author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S Abubucker</name>
</author>
<author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
<author><name sortKey="Yooseph, S" uniqKey="Yooseph S">S Yooseph</name>
</author>
<author><name sortKey="Methe, Ba" uniqKey="Methe B">BA Methé</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Henry, Cs" uniqKey="Henry C">CS Henry</name>
</author>
<author><name sortKey="Dejongh, M" uniqKey="Dejongh M">M DeJongh</name>
</author>
<author><name sortKey="Best, Aa" uniqKey="Best A">AA Best</name>
</author>
<author><name sortKey="Frybarger, Pm" uniqKey="Frybarger P">PM Frybarger</name>
</author>
<author><name sortKey="Linsay, B" uniqKey="Linsay B">B Linsay</name>
</author>
<author><name sortKey="Stevens, Rl" uniqKey="Stevens R">RL Stevens</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Henry, Cs" uniqKey="Henry C">CS Henry</name>
</author>
<author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R Overbeek</name>
</author>
<author><name sortKey="Xia, F" uniqKey="Xia F">F Xia</name>
</author>
<author><name sortKey="Best, Aa" uniqKey="Best A">AA Best</name>
</author>
<author><name sortKey="Glass, E" uniqKey="Glass E">E Glass</name>
</author>
<author><name sortKey="Gilbert, J" uniqKey="Gilbert J">J Gilbert</name>
</author>
<author><name sortKey="Larsen, P" uniqKey="Larsen P">P Larsen</name>
</author>
<author><name sortKey="Edwards, R" uniqKey="Edwards R">R Edwards</name>
</author>
<author><name sortKey="Disz, T" uniqKey="Disz T">T Disz</name>
</author>
<author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kalyanaraman, A" uniqKey="Kalyanaraman A">A Kalyanaraman</name>
</author>
<author><name sortKey="Aluru, S" uniqKey="Aluru S">S Aluru</name>
</author>
<author><name sortKey="Kothari, S" uniqKey="Kothari S">S Kothari</name>
</author>
<author><name sortKey="Brendel, V" uniqKey="Brendel V">V 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>
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<pmc article-type="product-review" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23800136</article-id>
<article-id pub-id-type="pmc">3695837</article-id>
<article-id pub-id-type="publisher-id">1471-2105-14-202</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-14-202</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Software</subject>
</subj-group>
</article-categories>
<title-group><article-title>MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Konwar</surname>
<given-names>Kishori M</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>kishori@mail.ubc.ca</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Hanson</surname>
<given-names>Niels W</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>nielsh@mail.ubc.ca</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Pagé</surname>
<given-names>Antoine P</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>appage@mail.ubc.ca</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A4"><name><surname>Hallam</surname>
<given-names>Steven J</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>shallam@mail.ubc.ca</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada</aff>
<aff id="I2"><label>2</label>
Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC Canada</aff>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>21</day>
<month>6</month>
<year>2013</year>
</pub-date>
<volume>14</volume>
<fpage>202</fpage>
<lpage>202</lpage>
<history><date date-type="received"><day>24</day>
<month>1</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>13</day>
<month>6</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2013 Konwar et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Konwar et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/14/202"></self-uri>
<abstract><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>
</abstract>
<kwd-group><kwd>Environmental pathway/Genome Database (ePGDB)</kwd>
<kwd>Metagenome</kwd>
<kwd>Pathway tools</kwd>
<kwd>PathoLogic</kwd>
<kwd>MetaCyc</kwd>
<kwd>Microbial community</kwd>
<kwd>Metabolism</kwd>
<kwd>Metabolic interaction networks</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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