Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Yang, Ying ^a   Jiang, Xiao Tao ^a   Zhang, Tong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; ARSENIC; NITROGEN;

ANTIBIOTIC RESISTANCE; ARTICLE; BLASTX; CONTROLLED STUDY; GENE TARGETING; INTERMETHOD COMPARISON; METAGENOMICS; NITROGEN METABOLISM; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TAXONOMIC IDENTIFICATION; UBLAST; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; MOLECULAR GENETICS; PROCEDURES; REPRODUCIBILITY; TIME;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATASETS AS TOPIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; REPRODUCIBILITY OF RESULTS; SOFTWARE; TIME FACTORS;

EID: 84908577899     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0110947     Document Type: Article

References (19)

1. Thomas T, Gilbert J, Meyer F (2012) Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2: 3.
2. Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB (2011) The real cost of sequencing: higher than you think! Genome Biol 12: 125.
3. Pennisi E (2011) Will computers crash genomics? Science 331: 666-668.
4. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467.
5. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, et al. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533-538.
6. Scholz MB, Lo CC, Chain PSG (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23: 9-15.
7. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
8. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
9. Ye Y, Choi JH, Tang H (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 12: 159.
10. Zhao Y, Tang H, Ye Y (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28: 125-126.
11. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
12. Yu K, Zhang T (2013) Construction of customized sub-databases from NCBI-nr database for rapid annotation of huge metagenomic datasets using a combined BLAST and MEGAN approach. PLoS ONE 8: e59831.
13. Liu B, Pop M (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Res 37: D443-D447.
14. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, et al. (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57: 3348-3357.
15. Yang Y, Li B, Ju F, Zhang T (2013) Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach. Environ Sci Technol 47: 10197-10205.
16. MacDonald NJ, Parks DH, Beiko RG (2012) Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res 40: e111.
17. Cai L, Yu K, Yang Y, Chen B-W, Li X-D, et al. (2013) Metagenomic exploration reveals high levels of microbial arsenic metabolism genes in activated sludge and coastal sediments. Appl Microbiol Biotechnol 97: 9579-9588.
18. Yang Y, Yu K, Xia Y, Lau FT, Tang DT, et al. (2014) Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biotechnol 98: 5709-5718.
19. Chao Y, Ma L, Yang Y, Ju F, Zhang XX, et al. (2013) Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment. Sci Rep 3: 3550.