publication . Article . Other literature type . 2016

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

David S. Wishart; David S. Wishart; Yongjie Liang; Jason R. Grant; David Arndt; Allison Pon; Tanvir Sajed; Ana Marcu;
Open Access
  • Published: 01 May 2016
  • Publisher: Oxford University Press (OUP)
Abstract
PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X ...
Subjects
free text keywords: Web Server issue, Web server, computer.software_genre, computer, Bacterial genome size, Graphical user interface, business.industry, business, User interface, Genetics, Genome browser, Biology, GenBank, Genome, Computer cluster, Programming language
Funded by
CIHR
Project
  • Funder: Canadian Institutes of Health Research (CIHR)
18 references, page 1 of 2

Casjens, S.. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol.. 2003; 49: 277-300 [OpenAIRE] [PubMed]

Zhou, Y., Liang, Y., Lynch, K.H., Dennis, J.J., Wishart, D.S.. PHAST: a fast phage search tool. Nucleic Acids Res.. 2011; 39: W347-W352 [OpenAIRE] [PubMed]

Schuster, S.C.. Next-generation sequencing transforms today's biology. Nat. Methods. 2008; 5: 16-18 [PubMed]

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.. Basic local alignment search tool. J. Mol. Biol.. 1990; 215: 403-410 [OpenAIRE] [PubMed]

Srividhya, K.V., Rao, G.V., Raghavenderan, L., Mehta, P., Prilusky, J., Manicka, S., Sussman, J.L., Krishnaswamy, S., Huang, D-S, Li, K, Irwin, GW. Database and comparative identification of prophages. Intelligent Control and Automation, Lecture Notes in Control and Information Sciences. 2006; 344: 863-868 [OpenAIRE]

Ester, M., Kriegel, H., Sander, J., Xu, X.. A density-based algorithm for discovering clusters in large spatial databases with noise. KDD-1996 Proceedings. 1996: 226-231

Bose, M., Barber, R.D.. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol. (Gedrukt). 2006; 6: 223-227 [PubMed]

Fouts, D.E.. Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res.. 2006; 34: 5839-5851 [OpenAIRE] [PubMed]

Lima-Mendez, G., Helden, J.V., Toussaint, A., Leplae, R.. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics. 2008; 24: 863-865 [PubMed]

Akhter, S., Aziz, R.K., Edwards, R.A.. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res.. 2012; 40: e126 [OpenAIRE] [PubMed]

Roux, S., Enault, F., Hurwitz, B.L., Sullivan, M.B.. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015; 3: e985 [OpenAIRE] [PubMed]

Kamke, J., Sczyrba, A., Ivanova, N., Schwientek, P., Rinke, C., Mavromatis, K., Woyke, T., Hentschel, U.. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J.. 2013; 7: 2287-2300 [OpenAIRE] [PubMed]

Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R.R., Stocker, R.. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014; 344: 416-420 [PubMed]

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L.. BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10: 421 [OpenAIRE] [PubMed]

Zhao, Y., Haixu, T., Yuzhen, Y.. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012; 28: 125-126 [OpenAIRE] [PubMed]

18 references, page 1 of 2
Abstract
PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X ...
Subjects
free text keywords: Web Server issue, Web server, computer.software_genre, computer, Bacterial genome size, Graphical user interface, business.industry, business, User interface, Genetics, Genome browser, Biology, GenBank, Genome, Computer cluster, Programming language
Funded by
CIHR
Project
  • Funder: Canadian Institutes of Health Research (CIHR)
18 references, page 1 of 2

Casjens, S.. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol.. 2003; 49: 277-300 [OpenAIRE] [PubMed]

Zhou, Y., Liang, Y., Lynch, K.H., Dennis, J.J., Wishart, D.S.. PHAST: a fast phage search tool. Nucleic Acids Res.. 2011; 39: W347-W352 [OpenAIRE] [PubMed]

Schuster, S.C.. Next-generation sequencing transforms today's biology. Nat. Methods. 2008; 5: 16-18 [PubMed]

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.. Basic local alignment search tool. J. Mol. Biol.. 1990; 215: 403-410 [OpenAIRE] [PubMed]

Srividhya, K.V., Rao, G.V., Raghavenderan, L., Mehta, P., Prilusky, J., Manicka, S., Sussman, J.L., Krishnaswamy, S., Huang, D-S, Li, K, Irwin, GW. Database and comparative identification of prophages. Intelligent Control and Automation, Lecture Notes in Control and Information Sciences. 2006; 344: 863-868 [OpenAIRE]

Ester, M., Kriegel, H., Sander, J., Xu, X.. A density-based algorithm for discovering clusters in large spatial databases with noise. KDD-1996 Proceedings. 1996: 226-231

Bose, M., Barber, R.D.. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol. (Gedrukt). 2006; 6: 223-227 [PubMed]

Fouts, D.E.. Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res.. 2006; 34: 5839-5851 [OpenAIRE] [PubMed]

Lima-Mendez, G., Helden, J.V., Toussaint, A., Leplae, R.. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics. 2008; 24: 863-865 [PubMed]

Akhter, S., Aziz, R.K., Edwards, R.A.. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res.. 2012; 40: e126 [OpenAIRE] [PubMed]

Roux, S., Enault, F., Hurwitz, B.L., Sullivan, M.B.. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015; 3: e985 [OpenAIRE] [PubMed]

Kamke, J., Sczyrba, A., Ivanova, N., Schwientek, P., Rinke, C., Mavromatis, K., Woyke, T., Hentschel, U.. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J.. 2013; 7: 2287-2300 [OpenAIRE] [PubMed]

Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R.R., Stocker, R.. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014; 344: 416-420 [PubMed]

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L.. BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10: 421 [OpenAIRE] [PubMed]

Zhao, Y., Haixu, T., Yuzhen, Y.. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012; 28: 125-126 [OpenAIRE] [PubMed]

18 references, page 1 of 2
Any information missing or wrong?Report an Issue