Comparison of metatranscriptomic samples based on k-tuple frequencies

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Wang, Ying ^a   Liu, Lin ^a   Chen, Lina ^a   Chen, Ting ^b   Sun, Fengzhu ^b  

^a XIAMEN UNIVERSITY   (China)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; INTERNET; METAGENOMICS; MICROBIOTA; SEAWATER; SOFTWARE; TRANSCRIPTOME; WATER MICROBIOLOGY;

EID: 84894288597     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084348     Document Type: Article

References (39)

1. Lozupone C, Lladser M, Knights D, Stombaugh J, Knight R (2007) UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169-172.
2. Smith T, Waterman M (1981) Comparison of biosequences. Adv Appl Math 2: 482-489.
3. Altschul S, Gish W, Miller W, Myers E, Lipman Dea (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
4. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, et al. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: 85.
5. Dick GJ, Clement BG, Webb SM, Fodrie FJ, Bargar JR, et al. (2009) Enzymatic microbial Mn oxidation in the Guaymas Basin deep-sea hydrothermal plume. Geochim Cosmochim Ac 73: 6517-6530.
6. Dick GJ, Tebo BM (2010) Microbial diversity and biogeochemistry of the Guaymas Basin hydrothermal plume. Environ Microbiol Rep 12: 1334-1347.
7. Ghosh T, Mohammed M, Rajasingh H, Chadaram S, Mande S (2011) HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences. BMC Bioinformatics 12: 59-69.
8. Gilbert JA, Field D, Swift P, Thomas S, Cummings D, et al. (2010) The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS ONE 5: e15545.
9. Gilbert JA, Meyer F, Schriml L, Joint IR, Mühling M, et al. (2010) Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Stand Genomic Sci 3: 183-193.
10. Jay McCarrena, Jamie W Beckera, Daniel J Repetac, Yanmei Shia, Curtis R Younga, et al. (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA 107: 16420-16427.
11. Mou X, Vila-Costa M, Sun S, Zhao W, Sharma S, et al. (2011) Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton. Environ Microbiol Rep 3: 798-806.
12. Poretsky R, Hewson I, Sun S, Allen A, Zehr J, et al. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11: 1358-1375.
13. Shi Y, Tyson GW, Eppley JM, DeLong EF (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5: 999-1013.
14. Karlin S, Mrazek J, Campbell A (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179: 3899-3913. (Pubitemid 27259908)
15. Blaisdell B (1986) A measure of the similarity of sets of sequences not requiring sequence alignment. Proc Natl Acad Sci USA 83: 5155-5159.
16. Hide W, Burke J, DA Vison D (1994) Biological evaluation of d2, an algorithm for highperformance sequence comparison. J Comput Biol 1: 199-215.
17. Miller R, Christoffels A, Gopalakrishnan C, Burke J, Ptitsyn A, et al. (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res 9: 1143-1155.
18. Kantorovitz MR, Robinson GE, Sinha S (2007) A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23: 249-255.
19. Reinert G, Chew D, Sun FZ, Waterman MS (2009) Alignment-free sequence comparison (I):Statistics and power. J Comput Biol 16: 1615-1634.
20. Wan L, Reinert G, Sun F, Waterman M (2010) Alignment-free sequence comparison (ii): theoretical power of comparison statistics. J Comput Biol 17: 1467-1490.
21. Dai Q, Wang T (2008) Comparison study on k-word statistical measures for protein: From sequence to sequence space. BMC Bioinformatics 9: 394.
22. Dai Q, Yang Y, Wang T (2008) Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics 24: 2296-2302.
23. Qi J, Wang B, Hao B (2004) Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 58: 1-11. (Pubitemid 38120400)
24. Song K, Ren J, Zhai Z, Liu X, Deng M, et al. (2013) Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. J Comput Biol 20: 64-79.
25. Jiang B, Song K, Ren J, Deng M, Sun F, et al. (2012) Comparison of metagenomic samples using sequence signatures. BMC Genomics 13: 730.
26. Pride D, Meinersmann R, Wassenaar T, Blaser M (2003) Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 13: 145-158.
27. Dalevi D, Dubhashi D, Hermansson M (2006) Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures. Bioinformatics 517-522. (Pubitemid 43372810)
28. Teeling H, Meyerdierks A, Bauer M, Amann R, Glöckner F (2004) Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol: 938-947. (Pubitemid 39123248)
29. Willner D, Thurber R, Rohwer F (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol 11: 1752-1766.
30. Reinert G, Chew D, Sun F (2009) Waterman MS: Alignment-free sequence comparison (I): statistics and power. J Comput Biol 12: 1615-1634.
31. Robinson DR, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53: 131-147.
32. Robinson DF, LR F (1981) Comparison of phylogenetic trees. Math Biosci 53: 131-147.
33. Schloss P, Handelsman J (2006) Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol 72: 2379-2384.
34. Murtagh F (1984) Complexities of hierarchic clutering algorithms: the state of the art. Comput Stat 1: 101-113.
35. Anderson M (2003) PCO: a FORTRAN computer program for principal coordinate analysis. New Zealand: Department of Statistics, University of Auckland. 7 p.
36. Xiong X, Frank D, Robertson C, Hung S, Markle J, et al. (2012) Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNASequencing. PLoS ONE 7: e36009.
37. Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I (2010) Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics 26: 420-425.
38. Margulies M, Egholm M, Altman WE, etc (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. (Pubitemid 41613494)
39. Zeng F, Jiang R, Chen T (2013) PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data. Nucl Acid Res 41: e136.