Introducing W.A.T.E.R.S.: A Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Hartman, Amber L ^a,c   Riddle, Sean ^b   McPhillips, Timothy ^b   Ludäscher, Bertram ^b   Eisen, Jonathan A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS SOFTWARES; AUTOMATED WORKFLOW; BIOLOGICAL INTERPRETATION; ECOLOGICAL ANALYSIS; FLEXIBLE AUTOMATION; INTEGRATED APPROACH; SEQUENCE ALIGNMENTS; VISUALIZATION TOOLS;

ALIGNMENT; BIOINFORMATICS; COMPUTER SOFTWARE; ECOLOGY; GENES; MICROBIOLOGY; RNA; TAXONOMIES;

TOOLS;

ARCHAEA; BACTERIA (MICROORGANISMS);

ARTICLE; COMPUTER PROGRAM; GENETICS; GENOMICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; RIBOSOME; RNA GENE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

BASE SEQUENCE; GENES, RRNA; GENOMICS; PHYLOGENY; RIBOSOMES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 77953313654     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-317     Document Type: Article

References (53)

1. Pace NR. A molecular view of microbial diversity and the biosphere. Science 1997, 276(5313):734-740. 10.1126/science.276.5313.734, 9115194.
2. Carney KM, Hungate BA, Drake BG, Megonigal JP. Altered soil microbial community at elevated CO(2) leads to loss of soil carbon. Proc Natl Acad Sci USA 2007, 104(12):4990-4995. 10.1073/pnas.0610045104, 1820881, 17360374.
3. Carney KM, Matson PA. The influence of tropical plant diversity and composition on soil microbial communities. Microb Ecol 2006, 52(2):226-238. 10.1007/s00248-006-9115-z, 16897297.
4. Schloter M, Bach HJ, Metz S, Sehy U, Munch JC. Influence of precision farming on the microbial community structure and functions in nitrogen turnover. Agriculture, Ecosystems & Environment 2003, 98(1-3):295-304.
5. Macfarlane S, Steed H, Macfarlane GT. Intestinal bacteria and inflammatory bowel disease. Crit Rev Clin Lab Sci 2009, 46(1):25-54. 10.1080/10408360802485792, 19107650.
6. Stecher B, Hardt WD. The role of microbiota in infectious disease. Trends Microbiol 2008, 16(3):107-114. 10.1016/j.tim.2007.12.008, 18280160.
7. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, et al. A core gut microbiome in obese and lean twins. Nature 2009, 457(7228):480-484. 10.1038/nature07540, 2677729, 19043404.
8. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444(7122):1022-1023. 10.1038/4441022a, 17183309.
9. Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR, Stahl DA, Felbeck H. Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16 S rRNA sequences. J Bacteriol 1988, 170(6):2506-2510. 211163, 3286609.
10. Stahl DA, Lane DJ, Olsen GJ, Pace NR. Characterization of a Yellowstone hot spring microbial community by 5 S rRNA sequences. Appl Environ Microbiol 1985, 49(6):1379-1384. 241732, 2409920.
11. Schmidt TM, DeLong EF, Pace NR. Analysis of a marine picoplankton community by 16 S rRNA gene cloning and sequencing. J Bacteriol 1991, 173(14):4371-4378. 208098, 2066334.
12. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16 S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990, 28(9):1942-1946. 268083, 2095137.
13. Medlin L, Elwood HJ, Stickel S, Sogin ML. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 1988, 71(2):491-499. 10.1016/0378-1119(88)90066-2, 3224833.
14. Woese CR, Stackebrandt E, Macke TJ, Fox GE. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985, 6:143-151.
15. Gutell RR, Weiser B, Woese CR, Noller HF. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol 1985, 32:155-216. full_text, 3911275.
16. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304(5667):66-74. 10.1126/science.1093857, 15001713.
17. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 2006, 311(5760):496-503. 10.1126/science.1120250, 16439655.
18. Grzymski JJ, Carter BJ, DeLong EF, Feldman RA, Ghadiri A, Murray AE. Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria. Appl Environ Microbiol 2006, 72(2):1532-1541. 10.1128/AEM.72.2.1532-1541.2006, 1392886, 16461708.
19. McDade-Ngutter C, Versalovic J, Alexander W, Hubbard VS, Starke-Reed P, Klein M, Raju T, Milner J, Davis C, Pontzer C, et al. National Institutes of Health Gastrointestinal Microbiota and Advances in Prebiotic and Probiotic Research conference summary. Gastroenterology 2009, 136(5):1473-1475. 10.1053/j.gastro.2009.03.042, 19328204.
20. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. New screening software shows that most recent large 16 S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 2006, 72(9):5734-5741. 10.1128/AEM.00556-06, 1563593, 16957188.
21. Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20(14):2317-2319. 10.1093/bioinformatics/bth226, 15073015.
22. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005, 71(12):8228-8235. 10.1128/AEM.71.12.8228-8235.2005, 1317376, 16332807.
23. Bowers S, McPhillips T, Wu M, Ludäscher B. Project Histories: Managing Data Provenance Across Collection-Oriented Scientific Workflow Runs. Data Integration in the Life Sciences 2007, 122-138.
24. Davidson SB, Boulakia SC, Eyal A, Ludäscher B, McPhillips TM, Bowers S, Anand MK, Freire J. Provenance in Scientific Workflow Systems. IEEE Data Eng Bull 2007, 30(4):44-50.
25. McPhillips T, Bowers S, Zinn D, Ludaescher B. Scientific workflow design for mere mortals. Future Generation Computer Systems 2009, 25(5):541-551.
26. Bowers S, Timothy M, Sean R, Manish A, Bertram L. Kepler/pPOD: Scientific Workflow and Provenance Support for Assembling the Tree of Life. International Provenance and Annotation Workshop (IPAW '08). Salt Lake City, Utah 2008,
27. McPhillips TM, Bowers S. An approach for pipelining nested collections in scientific workflows. SIGMOD Rec 2005, 34(3):12-17.
28. Peplies J, Kottmann R, Ludwig W, Glockner FO. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst Appl Microbiol 2008, 31(4):251-257. 10.1016/j.syapm.2008.08.003, 18786793.
29. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009, 75(23):7537-7541. 10.1128/AEM.01541-09, 2786419, 19801464.
30. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335-336. 10.1038/nmeth.f.303, 20383131.
31. Ludascher B, Altintas I, Bowers S, Cummings J, Critchlow T, Deelman E, DeRoure D, Freire J, Goble C, Jones M, et al. Scientific Process Automation and Workflow Management. Scientific Data Management 2009, Shoshani A.
32. Taylor I, Deelman E, Gannon D. Workflows for e-Science: Scientific Workflows for Grids. Springer 2006,
33. Ludascher B, Altintas I, Berkley C, Higgins D, Jaeger E, Jones M, E Lee A, Tao J, Zhao Y. Scientific workflow management and the Kepler system: Research Articles. Concurr Comput: Pract Exper 2006, 18(10):1039-1065.
34. The Kepler Project. , https://kepler-project.org/
35. Zinn D, Bowers S, McPhillips T, Ludascher B. Scientific workflow design with data assembly lines. Proceedings of the 4th Workshop on Workflows in Support of Large-Scale Science 2009, Portland, Oregon: ACM.
36. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25(10):1335-1337. 10.1093/bioinformatics/btp157, 2732312, 19307242.
37. Wu D, Hartman A, Ward N, Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 2008, 3(7):e2566. 10.1371/journal.pone.0002566, 2432038, 18596968.
38. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. At least 1 in 20 16 S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 2005, 71(12):7724-7736. 10.1128/AEM.71.12.7724-7736.2005, 1317345, 16332745.
39. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009, 26(7):1641-1650. 10.1093/molbev/msp077, 2693737, 19377059.
40. Howe K, Bateman A, Durbin R. QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 2002, 18(11):1546-1547. 10.1093/bioinformatics/18.11.1546, 12424131.
41. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
42. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008, 57(5):758-771. 10.1080/10635150802429642, 18853362.
43. Chao A. Non-parametric estimation of the number of classes in a population. Scand J Stat 1984, 11:265-270.
44. Shannon WWCE. The Mathematical Theory of Communication. 1949, Urbana, Illinois: University of Illinois.
45. Saldanha AJ. Java Treeview--extensible visualization of microarray data. Bioinformatics 2004, 20(17):3246-3248. 10.1093/bioinformatics/bth349, 15180930.
46. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
47. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16 S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006, 72(7):5069-5072. 10.1128/AEM.03006-05, 1489311, 16820507.
48. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science 2005, 308(5728):1635-1638. 10.1126/science.1110591, 1395357, 15831718.
49. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci USA 2009, 106(40):17187-17192. 10.1073/pnas.0904847106, 2746123, 19805153.
50. Anand MK, Bowers S, Ludascher B. A navigation model for exploring scientific workflow provenance graphs. Proceedings of the 4th Workshop on Workflows in Support of Large-Scale Science 2009, Portland, Oregon: ACM.
51. Freire J, Koop D, Santos E, Silva CT. Provenance for Computational Tasks: A Survey. Computing in Science and Engg 2008, 10(3):11-21.
52. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 2007, (35 Database):D169-172. 10.1093/nar/gkl889, 1669760, 17090583.
53. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35(21):7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.