FANTOM: Functional and taxonomic analysis of metagenomes

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Sanli, Kemal ^a,b   Karlsson, Fredrik H ^a   Nookaew, Intawat ^a   Nielsen, Jens ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Graphical User Interface (GUI); Metagenomics; Multivariate analysis; Statistical analysis; Visualization

Indexed keywords

BIOLOGICAL DATABASE; COMPARATIVE ANALYSIS; ECOSYSTEM FUNCTIONING; ENVIRONMENTAL SAMPLE; GRAPHICAL USER INTERFACES (GUI); HIERARCHICAL DATABASE; METADATA INFORMATION; METAGENOMES; METAGENOMICS; MULTI VARIATE ANALYSIS; ORTHOLOGY; PLATFORM INDEPENDENT; TAXONOMIC HIERARCHY;

FLOW VISUALIZATION; GRAPHICAL USER INTERFACES; METADATA; STATISTICAL METHODS;

COMPUTER SOFTWARE;

ARTICLE; BACTERIUM; CLASSIFICATION; COMPUTER PROGRAM; ENTERITIS; FACTUAL DATABASE; GENETIC DATABASE; GENETICS; HUMAN; METAGENOME; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; OBESITY;

BACTERIA; CLASSIFICATION; DATABASES, FACTUAL; DATABASES, GENETIC; HUMANS; INFLAMMATORY BOWEL DISEASES; METAGENOME; METAGENOMICS; OBESITY; SOFTWARE;

EID: 84873052852     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-38     Document Type: Article

References (27)

1. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet 2007, Washington (DC), http://www.ncbi.nlm.nih.gov/books/NBK54006.
2. Cox MP, Peterson DA, Biggs PJ. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinforma 2010, 11:485.
3. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27(6):863-864. 10.1093/bioinformatics/btr026, 3051327, 21278185.
4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
5. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011, 7(10):e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
6. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 2010, 11(5):473-483. 10.1093/bib/bbq015, 2943993, 20460430.
7. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol 2007, 5(3):e75. 10.1371/journal.pbio.0050075, 1821059, 17355175.
8. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 2008, 36:D534-D538. Database issue, 2238950, 17932063.
9. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma 2008, 9:386.
10. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 2011, 29(5):415-420. 10.1038/nbt.1823, 3367316, 21552244.
11. Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glockner FO, Field D. The genomic standards consortium: bringing standards to life for microbial ecology. ISME J 2011, 5(10):1565-1567. 10.1038/ismej.2011.39, 3176512, 21472015.
12. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17(3):377-386. 10.1101/gr.5969107, 1800929, 17255551.
13. Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P. SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics 2010, 26(23):2977-2978. 10.1093/bioinformatics/btq536, 20959381.
14. Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 2010, 26(6):715-721. 10.1093/bioinformatics/btq041, 20130030.
15. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 2010, 26(11):1463-1464. 10.1093/bioinformatics/btq166, 20395285.
16. Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci 2003, 14(6):927-930.
17. 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 2010, 7(5):335-336. 10.1038/nmeth.f.303, 3156573, 20383131.
18. 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.
19. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
20. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28(1):33-36. 10.1093/nar/28.1.33, 102395, 10592175.
21. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-D222. 10.1093/nar/gkp985, 2808889, 19920124.
22. Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003, 31(1):371-373. 10.1093/nar/gkg128, 165575, 12520025.
23. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464(7285):59-65. 10.1038/nature08821, 20203603.
24. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005, 102(31):11070-11075. 10.1073/pnas.0504978102, 1176910, 16033867.
25. Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C, Hardt PD. Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring) 2010, 18(1):190-195.
26. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, Flint HJ. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 2008, 32(11):1720-1724.
27. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 2008, 105(43):16731-16736. 10.1073/pnas.0804812105, 2575488, 18936492.