Advanced search
Publication Cover
Advances in Genomics and Genetics Volume 7, 2017 - Issue
Journal homepage
197
Views
0
CrossRef citations to date
0
Altmetric
Review

Use of profile hidden Markov models in viral discovery: current insights

Alejandro Reyes1 Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia;2 Department of Pathology and Immunology, Center for Genome Sciences and Systems Biology, Washington University in Saint Louis, St Louis, MO, USA;3 Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá,Colombia
,
João Marcelo P Alves4 Department of Parasitology, Institute of Biomedical Sciences
,
Alan Mitchell Durham5 Department of Computer Science, Institute of Mathematics and Statistics, Universidade de São Paulo, São Paulo,Brazil
&
Arthur Gruber4 Department of Parasitology, Institute of Biomedical SciencesCorrespondence[email protected]
Pages 29-45 | Published online: 14 Jul 2017

References

  • Durbin R, Eddy SR, Krogh A, Mitchison G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press; 1998.
  • Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 1998;8(3):163–167.
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–3402.
  • Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 1994;235(5):1501–1531.
  • Grose JH, Casjens SR. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology. 2014;468–470:421–443.
  • Koonin EV. Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol Direct. 2006;1:39.
  • Caston JR, Carrascosa JL. The basic architecture of viruses. Subcell Biochem. 2013;68:53–75.
  • Borderia AV, Stapleford KA, Vignuzzi M. RNA virus population diversity: implications for inter-species transmission. Curr Opin Virol. 2011;1(6):643–648.
  • Simmonds P. Genetic diversity and evolution of hepatitis C virus – 15 years on. J Gen Virol. 2004;85(Pt 11):3173–3188.
  • Jachiet PA, Colson P, Lopez P, Bapteste E. Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genome Biol Evol. 2014;6(9):2195–2205.
  • Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A. 1998;95(11):6073–6078.
  • Marz M, Beerenwinkel N, Drosten C, et al. Challenges in RNA virus bioinformatics. Bioinformatics. 2014;30(13):1793–1799.
  • Fancello L, Raoult D, Desnues C. Computational tools for viral metagenomics and their application in clinical research. Virology. 2012;434(2):162–174.
  • Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol. 1998;284(4):1201–1210.
  • Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, et al. Uncovering Earth’s virome. Nature. 2016;536(7617):425–430.
  • Sakowski EG, Munsell EV, Hyatt M, et al. Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses. Proc Natl Acad Sci U S A. 2014;111(44):15786–15791.
  • Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. ISME J. 2014;8(1):103–114.
  • Rowe JM, Fabre MF, Gobena D, Wilson WH, Wilhelm SW. Application of the major capsid protein as a marker of the phylogenetic diversity of Emiliania huxleyi viruses. FEMS Microbiol Ecol. 2011;76(2):373–380.
  • Hopkins M, Kailasan S, Cohen A, et al. Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein. ISME J. 2014;8(10):2093–2103.
  • Dwivedi B, Xue B, Lundin D, Edwards RA, Breitbart M. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol. 2013;13:33.
  • Hevroni G, Enav H, Rohwer F, Beja O. Diversity of viral photosystem-I psaA genes. ISME J. 2015;9(8):1892–1898.
  • Goldsmith DB, Parsons RJ, Beyene D, Salamon P, Breitbart M. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea. PeerJ. 2015;3:e997.
  • Greninger AL, Naccache SN, Federman S, et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015;7:99.
  • Boltz VF, Rausch J, Shao W, et al. Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA. Retrovirology. 2016;13(1):87.
  • Zou X, Tang G, Zhao X, et al. Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique. Sci China Life Sci. 2017;60(3):279–286.
  • Rodgers MA, Wilkerson E, Vallari A, et al. Sensitive next generation sequencing method reveals deep genetic diversity of HIV-1 in the Democratic Republic of the Congo. J Virol. 2017;91(6):pii:e01841-16.
  • Trebbien R, Pedersen SS, Vorborg K, Franck KT, Fischer TK. Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Euro Surveill. 2017;22(3):30445.
  • Hernandez D, Yu F, Huang X, Kirov S, Pant S, McPhee F. Impact of pre-existing NS5A-L31 or -Y93H minor variants on response rates in patients infected with HCV genotype-1b treated with daclatasvir/asunaprevir. Adv Ther. 2016;33(7):1169–1179.
  • Zhao Q, Wen Y, Jiang Y, et al. Next generation sequencing-based investigation of potential patient-to-patient hepatitis C virus transmission during hemodialytic treatment. PLoS One. 2016;11(1):e0147566.
  • Campo DS, Dimitrova Z, Yamasaki L, et al. Next-generation sequencing reveals large connected networks of intra-host HCV variants. BMC Genomics. 2014;15:(Suppl 5):S4.
  • Qiu P, Stevens R, Wei B, et al. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma. PLoS One. 2015;10(4):e0122082.
  • Sharma D, Priyadarshini P, Vrati S. Unraveling the web of viroinformatics: computational tools and databases in virus research. J Virol. 2015;89(3):1489–1501.
  • Brister JR, Ako-Adjei D, Bao Y, Blinkova O. NCBI viral genomes resource. Nucleic Acids Res. 2015;43(Database issue):D571–D577.
  • Finn RD, Coggill P, Eberhardt RY, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44(D1):D279–D285.
  • Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014;9(8):e105067.
  • Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 2017;45(Database issue):D491–D498.
  • Huerta-Cepas J, Szklarczyk D, Forslund K, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44(D1):D286–D293.
  • Kristensen DM, Cai X, Mushegian A. Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts. J Bacteriol. 2011;193(8):1806–1814.
  • Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV. Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J Bacteriol. 2013;195(5):941–950.
  • Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43(Database issue):D261–269.
  • Alves JM, de Oliveira AL, Sandberg TO, et al. GenSeed-HMM: a tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data. Front Microbiol. 2016;7:269.
  • Sobreira TJ, Gruber A. Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. Bioinformatics. 2008;24(15):1676–1680.
  • Zhang Y, Sun Y, Cole JR. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PLoS Comput Biol. 2014;10(8):e1003737.
  • Gregor I, Schonhuth A, McHardy AC. Snowball: strain aware gene assembly of metagenomes. Bioinformatics. 2016;32(17):i649–i657.
  • Li D, Huang Y, Leung HCM, Luo R, Ting HF, Lam TW. MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs. Lect Notes Comput Sci. 2016;9683:309.
  • Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome. 2015;3:32.
  • Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7(10):e1002195.
  • Zhong C, Edlund A, Yang Y, McLean JS, Yooseph S. Metagenome and metatranscriptome analyses using protein family profiles. PLoS Comput Biol. 2016;12(7):e1004991.
  • Hunt M, Gall A, Ong SH, et al. IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics. 2015;31(14):2374–2376.
  • Ruby JG, Bellare P, Derisi JL. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda). 2013;3(5):865–880.
  • Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtne W, Koopmans MP, Osterhaus ADME, Schürch AC. Recovering full-length viral genomes from metagenomes. Front Microbiol. 2015;6:1069.
  • Prosperi MC, Ciccozzi M, Fanti I, et al. A novel methodology for large-scale phylogeny partition. Nat Commun. 2011;2:321.
  • de Juan D, Pazos F, Valencia A. Emerging methods in protein co-evolution. Nat Rev Genet. 2013;14(4):249–261.
  • Yin Y, Fischer D. Identification and investigation of ORFans in the viral world. BMC Genomics. 2008;9:24.
  • Llorens C, Futami R, Covelli L, et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 2011;39(Database issue):D70–D74.
  • Foley B, Leitner T, Apetrei C, et al, editors. HIV Sequence Compendium 2013. New Mexico: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory; 2013.
  • Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–2948.
  • Gibson T, Higgins D, Thompson J [homepage on the Internet]. General help for CLUSTAL X (2.0). Available from: http://www.clustal.org/download/clustalx_help.html. Accessed May 22, 2017.

References

  • Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014;9(8):e105067.
  • Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 2017;45(Database issue):D491–D498.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.