PHASTER: a better, faster version of the PHAST phage search tool

Nucleic Acids Research

Volumn 44, Issue W1, 2016, Pages W16-W21

  Arndt, David ^a   Grant, Jason R ^a   Marcu, Ana ^a   Sajed, Tanvir ^a   Pon, Allison ^a   Liang, Yongjie ^a   Wishart, David S ^a,b,c  

^a Department of Computing Science ^*  (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIOPHAGE; BACTERIUM IDENTIFICATION; GENE SEQUENCE; MEASUREMENT ACCURACY; METAGENOMICS; NONHUMAN; PREDICTION; PREDICTIVE VALUE; SEQUENCE DATABASE; ALGORITHM; BACTERIUM; CHEMISTRY; COMPUTER GRAPHICS; GENE ONTOLOGY; GENETIC DATABASE; GENETICS; METABOLISM; MOLECULAR GENETICS; PLASMID; SEARCH ENGINE; SOFTWARE; TIME FACTOR; VIROLOGY;

VIRUS DNA;

ALGORITHMS; BACTERIA; BACTERIOPHAGES; COMPUTER GRAPHICS; DATABASES, GENETIC; DNA, VIRAL; GENE ONTOLOGY; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; PLASMIDS; SEARCH ENGINE; SOFTWARE; TIME FACTORS;

EID: 85009382739     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw387     Document Type: Article

References (18)

1. Casjens, S. (2003) Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol., 49, 277-300.
2. Zhou, Y., Liang, Y., Lynch, K.H., Dennis, J.J. and Wishart, D.S. (2011) PHAST: a fast phage search tool. Nucleic Acids Res., 39, W347-W352.
3. Schuster, S.C. (2008) Next-generation sequencing transforms today's biology. Nat. Methods, 5, 16-18.
4. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
5. Srividhya, K.V., Rao, G.V., Raghavenderan, L., Mehta, P., Prilusky, J., Manicka, S., Sussman, J.L. and Krishnaswamy, S. (2006) Database and comparative identification of prophages. In: Huang, D-S, Li, K and Irwin, GW (eds). Intelligent Control and Automation, Lecture Notes in Control and Information Sciences. Springer, Berlin, Vol. 344, pp. 863-868.
6. Ester, M., Kriegel, H., Sander, J. and Xu, X. (1996) A density-based algorithm for discovering clusters in large spatial databases with noise. In: KDD-1996 Proceedings. AAAI Press, Menlo Park, pp. 226-231.
7. Bose, M. and Barber, R.D. (2006) Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol. (Gedrukt), 6, 223-227.
8. Fouts, D.E. (2006) Phage Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res., 34, 5839-5851.
9. Lima-Mendez, G., Helden, J.V., Toussaint, A. and Leplae, R. (2008) Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics, 24, 863-865.
10. Akhter, S., Aziz, R.K. and Edwards, R.A. (2012) PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res., 40, e126.
11. Roux, S., Enault, F., Hurwitz, B.L. and Sullivan, M.B. (2015) VirSorter: mining viral signal from microbial genomic data. PeerJ, 3, e985.
12. Kamke, J., Sczyrba, A., Ivanova, N., Schwientek, P., Rinke, C., Mavromatis, K., Woyke, T. and Hentschel, U. (2013) Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J., 7, 2287-2300.
13. Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R.R., Stocker, R. et al. (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science, 344, 416-420.
14. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
15. Zhao, Y., Haixu, T. and Yuzhen, Y. (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics, 28, 125-126.
16. Rho, M., Tang, H. and Ye, Y. (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res., 38, e191.
17. Pruitt, K.D., Brown, G.R., Hiatt, S.M., Thibaud-Nissen, F., Astashyn, A., Ermolaeva, O., Farrell, C.M., Hart, J., Landrum, M.J., McGarvey, K.M. et al. (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res., 42, D756-D763.
18. Fu, L., Niu, B., Zhu, Z., Wu, S. and Li, W. (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150-3152