IDBA-MTP: A hybrid metatranscriptomic assembler based on protein information

Journal of Computational Biology

Volumn 22, Issue 5, 2015, Pages 367-376

  Leung, Henry C M ^a   Yiu, Siu Ming ^a   Chin, Francis Y L ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

assembling; metatranscriptomic reads; next generation sequencing; protein sequence alignment

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; MESSENGER RNA; PROTEOME; TRANSCRIPTOME;

ALGORITHM; CHEMISTRY; COMPUTER PROGRAM; CONTIG MAPPING; DATA MINING; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; MICROBIAL CONSORTIUM; PROCEDURES; STATISTICS AND NUMERICAL DATA;

ALGORITHMS; BACTERIAL PROTEINS; CONTIG MAPPING; DATA MINING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MICROBIAL CONSORTIA; PROTEOME; RNA, BACTERIAL; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTOME;

EID: 84929657413     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2014.0139     Document Type: Article

References (24)

1. Benson, D., Karsch-Mizrachi, I., Lipman, D., et al. 2000. GenBank. Nucleic Acids Res. 28, 15-18
2. Booijink, C., Boekhorst, J., Zoetendal, E., et al. 2010. Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl. Environ. Microbiol. 76, 5533-5540
3. Bosch, J., and Grody, W. 2008. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J. Mol. Diagn. 10, 484-492
4. Eisen, J. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 5, e82
5. Finn, R., Tate, J., Mistry, J., et al. 2000. The Pfam protein families database. Nucleic Acids Res. 28, 263-266
6. Frias-Lopez, J., Shi, Y., Tyson, G., et al. 2008. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 105, 3805-3810
7. Fullwood, M., Wei, C., Liu, E., et al. 2009. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 19, 521-532
8. Gilbert, J., Field, D., Huang, Y., et al. 2008. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3, e3042
9. Glazer, A., and Kechris, K. 2009. Conserved amino acid sequence features in the a subunits of MoFe, VFe, and FeFe nitrogenases. PLoS ONE 4, e6136
10. Grabherr, M., Haas, B., Yassour, M., et al. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644-652
11. Henikoff, S., and Henikoff, J. 1992. Amino acid substitution matrices from protein blocks. PNAS 89, 10915-10919
12. Kent, J. 2002. BLAT-The BLAST-like alignment tool. Genome Res. 12, 656-664
13. Leung, H., Yiu, S., Parkinson, J., et al. 2013. IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology. J. Comput. Biol. 20, 540-550
14. Morozova, O., and Marra, M. 2008. Applications of next-generation sequencing technologies in functional genomics. Genomics 92, 255-264
15. Parro, V., Moreno-Paz, M., and Gonzalez-Toril, E. 2007. Analysis of environmental transcriptomes by DNA microarrays. Env. Microbiol. 9, 453-464
16. Peng, Y., Leung, H., Yiu, S., et al. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428
17. Pettersson, E., Lundeberg, J., and Ahmadian, A 2009. Generations of sequencing technologies. Genomics 93, 105-111
18. Poretsky, R., Bano, N., Buchan, A., et al. 2005. Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71, 4121-4126
19. Poretsky, R., Sun, S., Mou, X., et al. 2010. Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environ. Microbiol. 12, 616-627
20. Qin, J., Li, R., Raes, J., et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65
21. Schulz, M., Zerbino, D., Vingron, M., et al. 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086-1092
22. Tartar, A., Wheeler, M., Zhou, X., et al. 2009. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. Biotechnol. Biofuels 2, 25
23. Tatusov, R., Koonin, E., and Lipman, D. 1997. A genomic perspective on protein families. Science 278, 631-637
24. Xiong, X., Frank, D., Robertson, C., et al. 2012. Generation and analysis of a mouse intestinal metatranscriptome through illumina based RNA-sequencing. PLoS ONE 7, e36009