Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies
Identifieur interne : 000495 ( Pmc/Checkpoint ); précédent : 000494; suivant : 000496Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies
Auteurs : H. James Tripp [États-Unis] ; Ian Hewson [États-Unis] ; Sam Boyarsky [États-Unis] ; Joshua M. Stuart [États-Unis] ; Jonathan P. Zehr [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2011.
Abstract
In the course of analyzing 9 522 746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, ‘Cw-hydrolase’) uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.
Url:
DOI: 10.1093/nar/gkr576
PubMed: 21771858
PubMed Central: 3203614
Affiliations:
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Zehr</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ocean Sciences, University of California, Santa Cruz, CA 95064</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21771858</idno><idno type="pmc">3203614</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203614</idno><idno type="RBID">PMC:3203614</idno><idno type="doi">10.1093/nar/gkr576</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000587</idno><idno type="wicri:Area/Pmc/Curation">000587</idno><idno type="wicri:Area/Pmc/Checkpoint">000495</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies</title><author><name sortKey="Tripp, H James" sort="Tripp, H James" uniqKey="Tripp H" first="H. James" last="Tripp">H. James Tripp</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ocean Sciences, University of California, Santa Cruz, CA 95064</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Hewson, Ian" sort="Hewson, Ian" uniqKey="Hewson I" first="Ian" last="Hewson">Ian Hewson</name><affiliation wicri:level="4"><nlm:aff id="AFF1">Department of Microbiology, Cornell University, Wing Hall 403, Ithaca, NY 14853, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, Cornell University, Wing Hall 403, Ithaca, NY 14853</wicri:regionArea><placeName><region type="state">État de New York</region><settlement type="city">Ithaca (New York)</settlement></placeName><orgName type="university">Université Cornell</orgName></affiliation></author><author><name sortKey="Boyarsky, Sam" sort="Boyarsky, Sam" uniqKey="Boyarsky S" first="Sam" last="Boyarsky">Sam Boyarsky</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ocean Sciences, University of California, Santa Cruz, CA 95064</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Stuart, Joshua M" sort="Stuart, Joshua M" uniqKey="Stuart J" first="Joshua M." last="Stuart">Joshua M. Stuart</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ocean Sciences, University of California, Santa Cruz, CA 95064</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zehr, Jonathan P" sort="Zehr, Jonathan P" uniqKey="Zehr J" first="Jonathan P." last="Zehr">Jonathan P. Zehr</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ocean Sciences, University of California, Santa Cruz, CA 95064</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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>In the course of analyzing 9 522 746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, ‘Cw-hydrolase’) uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Roberts, R" uniqKey="Roberts R">R Roberts</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woese, Cr" uniqKey="Woese C">CR Woese</name></author><author><name sortKey="Fox, Ge" uniqKey="Fox G">GE Fox</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dunn, Jj" uniqKey="Dunn J">JJ Dunn</name></author><author><name sortKey="Studier, Fw" uniqKey="Studier F">FW Studier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ginsburg, D" uniqKey="Ginsburg D">D Ginsburg</name></author><author><name sortKey="Steitz, Ja" uniqKey="Steitz J">JA Steitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smitt, Ww" uniqKey="Smitt W">WW Smitt</name></author><author><name sortKey="Vlak, Jm" uniqKey="Vlak J">JM Vlak</name></author><author><name sortKey="Schiphof, R" uniqKey="Schiphof R">R Schiphof</name></author><author><name sortKey="Rozijn, Th" uniqKey="Rozijn T">TH Rozijn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Udem, Sa" uniqKey="Udem S">SA Udem</name></author><author><name sortKey="Warner, Jr" uniqKey="Warner J">JR Warner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brosius, J" uniqKey="Brosius J">J Brosius</name></author><author><name sortKey="Dull, Tj" uniqKey="Dull T">TJ Dull</name></author><author><name sortKey="Noller, Hf" uniqKey="Noller H">HF Noller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brosius, J" uniqKey="Brosius J">J Brosius</name></author><author><name sortKey="Palmer, Ml" uniqKey="Palmer M">ML Palmer</name></author><author><name sortKey="Kennedy, Pj" uniqKey="Kennedy P">PJ Kennedy</name></author><author><name sortKey="Noller, Hf" uniqKey="Noller H">HF Noller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brownlee, Gg" uniqKey="Brownlee G">GG Brownlee</name></author><author><name sortKey="Sanger, F" uniqKey="Sanger F">F Sanger</name></author><author><name sortKey="Barrell, Bg" uniqKey="Barrell B">BG Barrell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carbon, P" uniqKey="Carbon P">P Carbon</name></author><author><name sortKey="Ehresmann, C" uniqKey="Ehresmann C">C Ehresmann</name></author><author><name sortKey="Ehresmann, B" uniqKey="Ehresmann B">B Ehresmann</name></author><author><name sortKey="Ebel, Jp" uniqKey="Ebel J">JP Ebel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Georgiev, Oi" uniqKey="Georgiev O">OI Georgiev</name></author><author><name sortKey="Nikolaev, N" uniqKey="Nikolaev N">N Nikolaev</name></author><author><name sortKey="Hadjiolov, Aa" uniqKey="Hadjiolov A">AA Hadjiolov</name></author><author><name sortKey="Skryabin, Kg" uniqKey="Skryabin K">KG Skryabin</name></author><author><name sortKey="Zakharyev, Vm" uniqKey="Zakharyev V">VM Zakharyev</name></author><author><name sortKey="Bayev, Aa" uniqKey="Bayev A">AA Bayev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hindley, J" uniqKey="Hindley J">J Hindley</name></author><author><name sortKey="Page, Sm" uniqKey="Page S">SM Page</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rubin, Gm" uniqKey="Rubin G">GM Rubin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rubtsov, Pm" uniqKey="Rubtsov P">PM Rubtsov</name></author><author><name sortKey="Musakhanov, Mm" uniqKey="Musakhanov M">MM Musakhanov</name></author><author><name sortKey="Zakharyev, Vm" uniqKey="Zakharyev V">VM Zakharyev</name></author><author><name sortKey="Krayev, As" uniqKey="Krayev A">AS Krayev</name></author><author><name sortKey="Skryabin, Kg" uniqKey="Skryabin K">KG Skryabin</name></author><author><name sortKey="Bayev, Aa" uniqKey="Bayev A">AA Bayev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tenson, T" uniqKey="Tenson T">T Tenson</name></author><author><name sortKey="Deblasio, A" uniqKey="Deblasio A">A DeBlasio</name></author><author><name sortKey="Mankin, A" uniqKey="Mankin A">A Mankin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mitschke, J" uniqKey="Mitschke J">J Mitschke</name></author><author><name sortKey="Georg, J" uniqKey="Georg J">J Georg</name></author><author><name sortKey="Scholz, I" uniqKey="Scholz I">I Scholz</name></author><author><name sortKey="Sharma, Cm" uniqKey="Sharma C">CM Sharma</name></author><author><name sortKey="Dienst, D" uniqKey="Dienst D">D Dienst</name></author><author><name sortKey="Bantscheff, J" uniqKey="Bantscheff J">J Bantscheff</name></author><author><name sortKey="Voss, B" uniqKey="Voss B">B Voss</name></author><author><name sortKey="Steglich, C" uniqKey="Steglich C">C Steglich</name></author><author><name sortKey="Wilde, A" uniqKey="Wilde A">A Wilde</name></author><author><name sortKey="Vogel, J" uniqKey="Vogel J">J Vogel</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="Coelho, Ps" uniqKey="Coelho P">PS Coelho</name></author><author><name sortKey="Bryan, Ac" uniqKey="Bryan A">AC Bryan</name></author><author><name sortKey="Kumar, A" uniqKey="Kumar A">A Kumar</name></author><author><name sortKey="Shadel, Gs" uniqKey="Shadel G">GS Shadel</name></author><author><name sortKey="Snyder, M" uniqKey="Snyder M">M Snyder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mauro, Vp" uniqKey="Mauro V">VP Mauro</name></author><author><name sortKey="Edelman, Gm" uniqKey="Edelman G">GM Edelman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chooi, Wy" uniqKey="Chooi W">WY Chooi</name></author><author><name sortKey="Leiby, Kr" uniqKey="Leiby K">KR Leiby</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kermekchiev, M" uniqKey="Kermekchiev M">M Kermekchiev</name></author><author><name sortKey="Ivanova, L" uniqKey="Ivanova L">L Ivanova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scharf, Me" uniqKey="Scharf M">ME Scharf</name></author><author><name sortKey="Wu Scharf, D" uniqKey="Wu Scharf D">D Wu-Scharf</name></author><author><name sortKey="Zhou, X" uniqKey="Zhou X">X Zhou</name></author><author><name sortKey="Pittendrigh, Br" uniqKey="Pittendrigh B">BR Pittendrigh</name></author><author><name sortKey="Bennett, Gw" uniqKey="Bennett G">GW Bennett</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Finn, Rd" uniqKey="Finn R">RD Finn</name></author><author><name sortKey="Mistry, J" uniqKey="Mistry J">J Mistry</name></author><author><name sortKey="Tate, J" uniqKey="Tate J">J Tate</name></author><author><name sortKey="Coggill, P" uniqKey="Coggill P">P Coggill</name></author><author><name sortKey="Heger, A" uniqKey="Heger A">A Heger</name></author><author><name sortKey="Pollington, Je" uniqKey="Pollington J">JE Pollington</name></author><author><name sortKey="Gavin, Ol" uniqKey="Gavin O">OL Gavin</name></author><author><name sortKey="Gunasekaran, P" uniqKey="Gunasekaran P">P Gunasekaran</name></author><author><name sortKey="Ceric, G" uniqKey="Ceric G">G Ceric</name></author><author><name sortKey="Forslund, K" uniqKey="Forslund K">K Forslund</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shi, Y" uniqKey="Shi Y">Y Shi</name></author><author><name sortKey="Tyson, Gw" uniqKey="Tyson G">GW Tyson</name></author><author><name sortKey="Delong, Ef" uniqKey="Delong E">EF DeLong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, S" uniqKey="Sun S">S Sun</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author><author><name sortKey="Altintas, I" uniqKey="Altintas I">I Altintas</name></author><author><name sortKey="Lin, A" uniqKey="Lin A">A Lin</name></author><author><name sortKey="Peltier, S" uniqKey="Peltier S">S Peltier</name></author><author><name sortKey="Stocks, K" uniqKey="Stocks K">K Stocks</name></author><author><name sortKey="Allen, Ee" uniqKey="Allen E">EE Allen</name></author><author><name sortKey="Ellisman, M" uniqKey="Ellisman M">M Ellisman</name></author><author><name sortKey="Grethe, J" uniqKey="Grethe J">J Grethe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rutherford, K" uniqKey="Rutherford K">K Rutherford</name></author><author><name sortKey="Parkhill, J" uniqKey="Parkhill J">J Parkhill</name></author><author><name sortKey="Crook, J" uniqKey="Crook J">J Crook</name></author><author><name sortKey="Horsnell, T" uniqKey="Horsnell T">T Horsnell</name></author><author><name sortKey="Rice, P" uniqKey="Rice P">P Rice</name></author><author><name sortKey="Rajandream, Ma" uniqKey="Rajandream M">MA Rajandream</name></author><author><name sortKey="Barrell, B" uniqKey="Barrell B">B Barrell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name></author><author><name sortKey="Chen, Im" uniqKey="Chen I">IM Chen</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="Szeto, E" uniqKey="Szeto E">E Szeto</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="Anderson, I" uniqKey="Anderson I">I Anderson</name></author><author><name sortKey="Lykidis, A" uniqKey="Lykidis A">A Lykidis</name></author><author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</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 Glockner</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="Lagesen, K" uniqKey="Lagesen K">K Lagesen</name></author><author><name sortKey="Hallin, P" uniqKey="Hallin P">P Hallin</name></author><author><name sortKey="Rodland, Ea" uniqKey="Rodland E">EA Rodland</name></author><author><name sortKey="Staerfeldt, Hh" uniqKey="Staerfeldt H">HH Staerfeldt</name></author><author><name sortKey="Rognes, T" uniqKey="Rognes T">T Rognes</name></author><author><name sortKey="Ussery, Dw" uniqKey="Ussery D">DW Ussery</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liolios, K" uniqKey="Liolios K">K Liolios</name></author><author><name sortKey="Chen, Im" uniqKey="Chen I">IM Chen</name></author><author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</name></author><author><name sortKey="Tavernarakis, N" uniqKey="Tavernarakis N">N Tavernarakis</name></author><author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name></author><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name></author><author><name sortKey="Kyrpides, Nc" uniqKey="Kyrpides N">NC Kyrpides</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kawarabayasi, Y" uniqKey="Kawarabayasi Y">Y Kawarabayasi</name></author><author><name sortKey="Sawada, M" uniqKey="Sawada M">M Sawada</name></author><author><name sortKey="Horikawa, H" uniqKey="Horikawa H">H Horikawa</name></author><author><name sortKey="Haikawa, Y" uniqKey="Haikawa Y">Y Haikawa</name></author><author><name sortKey="Hino, Y" uniqKey="Hino Y">Y Hino</name></author><author><name sortKey="Yamamoto, S" uniqKey="Yamamoto S">S Yamamoto</name></author><author><name sortKey="Sekine, M" uniqKey="Sekine M">M Sekine</name></author><author><name sortKey="Baba, S" uniqKey="Baba S">S Baba</name></author><author><name sortKey="Kosugi, H" uniqKey="Kosugi H">H Kosugi</name></author><author><name sortKey="Hosoyama, A" uniqKey="Hosoyama A">A Hosoyama</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kunst, F" uniqKey="Kunst F">F Kunst</name></author><author><name sortKey="Ogasawara, N" uniqKey="Ogasawara N">N Ogasawara</name></author><author><name sortKey="Moszer, I" uniqKey="Moszer I">I Moszer</name></author><author><name sortKey="Albertini, Am" uniqKey="Albertini A">AM Albertini</name></author><author><name sortKey="Alloni, G" uniqKey="Alloni G">G Alloni</name></author><author><name sortKey="Azevedo, V" uniqKey="Azevedo V">V Azevedo</name></author><author><name sortKey="Bertero, Mg" uniqKey="Bertero M">MG Bertero</name></author><author><name sortKey="Bessieres, P" uniqKey="Bessieres P">P Bessieres</name></author><author><name sortKey="Bolotin, A" uniqKey="Bolotin A">A Bolotin</name></author><author><name sortKey="Borchert, S" uniqKey="Borchert S">S Borchert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Medigue, C" uniqKey="Medigue C">C Medigue</name></author><author><name sortKey="Moszer, I" uniqKey="Moszer I">I Moszer</name></author><author><name sortKey="Viari, A" uniqKey="Viari A">A Viari</name></author><author><name sortKey="Danchin, A" uniqKey="Danchin A">A Danchin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Medigue, C" uniqKey="Medigue C">C Medigue</name></author><author><name sortKey="Rouxel, T" uniqKey="Rouxel T">T Rouxel</name></author><author><name sortKey="Vigier, P" uniqKey="Vigier P">P Vigier</name></author><author><name sortKey="Henaut, A" uniqKey="Henaut A">A Henaut</name></author><author><name sortKey="Danchin, A" uniqKey="Danchin A">A Danchin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Staden, R" uniqKey="Staden R">R Staden</name></author><author><name sortKey="Mclachlan, Ad" uniqKey="Mclachlan A">AD McLachlan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krogh, A" uniqKey="Krogh A">A Krogh</name></author><author><name sortKey="Mian, Is" uniqKey="Mian I">IS Mian</name></author><author><name sortKey="Haussler, D" uniqKey="Haussler D">D Haussler</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, Hy" uniqKey="Chuang H">HY 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 Crecy-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="Bakke, P" uniqKey="Bakke P">P Bakke</name></author><author><name sortKey="Carney, N" uniqKey="Carney N">N Carney</name></author><author><name sortKey="Deloache, W" uniqKey="Deloache W">W Deloache</name></author><author><name sortKey="Gearing, M" uniqKey="Gearing M">M Gearing</name></author><author><name sortKey="Ingvorsen, K" uniqKey="Ingvorsen K">K Ingvorsen</name></author><author><name sortKey="Lotz, M" uniqKey="Lotz M">M Lotz</name></author><author><name sortKey="Mcnair, J" uniqKey="Mcnair J">J McNair</name></author><author><name sortKey="Penumetcha, P" uniqKey="Penumetcha P">P Penumetcha</name></author><author><name sortKey="Simpson, S" uniqKey="Simpson S">S Simpson</name></author><author><name sortKey="Voss, L" uniqKey="Voss L">L Voss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name></author><author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</name></author><author><name sortKey="Ivanova, Nn" uniqKey="Ivanova N">NN Ivanova</name></author><author><name sortKey="Chen, Im" uniqKey="Chen I">IM Chen</name></author><author><name sortKey="Chu, K" uniqKey="Chu K">K Chu</name></author><author><name sortKey="Kyrpides, Nc" uniqKey="Kyrpides N">NC Kyrpides</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scheunemann, Ae" uniqKey="Scheunemann A">AE Scheunemann</name></author><author><name sortKey="Graham, Wd" uniqKey="Graham W">WD Graham</name></author><author><name sortKey="Vendeix, Fa" uniqKey="Vendeix F">FA Vendeix</name></author><author><name sortKey="Agris, Pf" uniqKey="Agris P">PF Agris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maguire, Ba" uniqKey="Maguire B">BA Maguire</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carter, Ap" uniqKey="Carter A">AP Carter</name></author><author><name sortKey="Clemons, Wm" uniqKey="Clemons W">WM Clemons</name></author><author><name sortKey="Brodersen, De" uniqKey="Brodersen D">DE Brodersen</name></author><author><name sortKey="Morgan Warren, Rj" uniqKey="Morgan Warren R">RJ Morgan-Warren</name></author><author><name sortKey="Wimberly, Bt" uniqKey="Wimberly B">BT Wimberly</name></author><author><name sortKey="Ramakrishnan, V" uniqKey="Ramakrishnan V">V Ramakrishnan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mehta, R" uniqKey="Mehta R">R Mehta</name></author><author><name sortKey="Champney, Ws" uniqKey="Champney W">WS Champney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="David Eden, H" uniqKey="David Eden H">H David-Eden</name></author><author><name sortKey="Mankin, As" uniqKey="Mankin A">AS Mankin</name></author><author><name sortKey="Mandel Gutfreund, Y" uniqKey="Mandel Gutfreund Y">Y Mandel-Gutfreund</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author><author><name sortKey="Duc, Ac" uniqKey="Duc A">AC Duc</name></author><author><name sortKey="Klosi, E" uniqKey="Klosi E">E Klosi</name></author><author><name sortKey="Pattabiraman, S" uniqKey="Pattabiraman S">S Pattabiraman</name></author><author><name sortKey="Spaller, Mr" uniqKey="Spaller M">MR Spaller</name></author><author><name sortKey="Chow, Cs" uniqKey="Chow C">CS Chow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Warner, Jr" uniqKey="Warner J">JR Warner</name></author><author><name sortKey="Vilardell, J" uniqKey="Vilardell J">J Vilardell</name></author><author><name sortKey="Sohn, Jh" uniqKey="Sohn J">JH Sohn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kjeldgaard, No" uniqKey="Kjeldgaard N">NO Kjeldgaard</name></author><author><name sortKey="Gausing, K" uniqKey="Gausing K">K Gausing</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21771858</article-id><article-id pub-id-type="pmc">3203614</article-id><article-id pub-id-type="doi">10.1093/nar/gkr576</article-id><article-id pub-id-type="publisher-id">gkr576</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genomics</subject></subj-group></article-categories><title-group><article-title>Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tripp</surname><given-names>H. James</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hewson</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Boyarsky</surname><given-names>Sam</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Stuart</surname><given-names>Joshua M.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zehr</surname><given-names>Jonathan P.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA and<sup>2</sup>Department of Microbiology, Cornell University, Wing Hall 403, Ithaca, NY 14853, USA</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>831 459 4009</phone>; Fax: <fax>831 459 4882</fax>; Email: <email>zehrj@ucsc.edu</email></corresp></author-notes><pmc-comment>For NAR both ppub and collection dates generated for PMC processing 1/27/05 beck</pmc-comment>
<pub-date pub-type="collection"><month>11</month><year>2011</year></pub-date><pub-date pub-type="ppub"><month>11</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>19</day><month>7</month><year>2011</year></pub-date><pub-date pub-type="pmc-release"><day>19</day><month>7</month><year>2011</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>39</volume><issue>20</issue><fpage>8792</fpage><lpage>8802</lpage><history><date date-type="received"><day>24</day><month>3</month><year>2011</year></date><date date-type="rev-recd"><day>24</day><month>6</month><year>2011</year></date><date date-type="accepted"><day>27</day><month>6</month><year>2011</year></date></history><permissions><copyright-statement>© The Author(s) 2011. Published by Oxford University Press.</copyright-statement><copyright-year>2011</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>In the course of analyzing 9 522 746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, ‘Cw-hydrolase’) uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.</p></abstract><counts><page-count count="11"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li><li>État de New York</li></region><settlement><li>Ithaca (New York)</li></settlement><orgName><li>Université Cornell</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Tripp, H James" sort="Tripp, H James" uniqKey="Tripp H" first="H. James" last="Tripp">H. James Tripp</name></region><name sortKey="Boyarsky, Sam" sort="Boyarsky, Sam" uniqKey="Boyarsky S" first="Sam" last="Boyarsky">Sam Boyarsky</name><name sortKey="Hewson, Ian" sort="Hewson, Ian" uniqKey="Hewson I" first="Ian" last="Hewson">Ian Hewson</name><name sortKey="Stuart, Joshua M" sort="Stuart, Joshua M" uniqKey="Stuart J" first="Joshua M." last="Stuart">Joshua M. Stuart</name><name sortKey="Zehr, Jonathan P" sort="Zehr, Jonathan P" uniqKey="Zehr J" first="Jonathan P." last="Zehr">Jonathan P. Zehr</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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