Advertisement

Bioinformatics in Next-Generation Genome Sequencing

  • Satendra Singh
  • Anjali Rao
  • Pallavi Mishra
  • Arvind Kumar Yadav
  • Ranjeet Maurya
  • Sukhdeep Kaur
  • Gitanjali Tandon
Chapter

Abstract

In the present era, genomics represent a crucial role in the field of life sciences. Advancements in genomics and the development of high-throughput techniques facilitate the characterization of a wide range of genes according to their functions such as regulation of genes, metabolic pathways, and their reconstruction. In the era of genomics we face the challenge of storage and analysis of a huge amount of important data. Even in this early stage of the era there are many commercial techniques and tools/software available to analyze next-generation sequencing (NGS) data. All of these programs can be used for many uses such as sequence alignments, polymorphism detection, and functional and structural comparative genomics. In this chapter, we focus on advances in bioinformatics and also computational biology in genome sequencing and NGS data analysis and on the potential applications for the efficient collection, storage, and analysis of the huge amount of genomic data generated by researchers and the information retrieved from different sources and web browsers in relation to NGS analysis.

Keywords

Bioinformatics Genomics Next-generation sequencing Technologies 

Notes

Acknowledgements

The authors are grateful to the Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly Allahabad Agriculture Institute) (Deemed-to-be-University), Allahabad, India, for providing the facilities and support to complete the work.

References

  1. Alkan C et al (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41:1061–1067CrossRefPubMedPubMedCentralGoogle Scholar
  2. Andersson R et al (2014) An atlas of active enhancers across human cell types and tissues. Nature 507:455–461CrossRefPubMedPubMedCentralGoogle Scholar
  3. Ashelford K et al (2011) Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol 12:1CrossRefGoogle Scholar
  4. Auffray C et al (2009) Systems medicine: the future of medical genomics and healthcare. Genome Med 1:1CrossRefGoogle Scholar
  5. Blat Y, Kleckner N (1999) Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell 98:249–259CrossRefPubMedGoogle Scholar
  6. Brulc JM et al (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106:1948–1953CrossRefPubMedPubMedCentralGoogle Scholar
  7. Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci U S A 81:1991–1995CrossRefPubMedPubMedCentralGoogle Scholar
  8. Deng W et al (2008) The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review. Mol Biol Rep 35:265–274CrossRefPubMedGoogle Scholar
  9. ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia of DNA elements) project. Science 306:636–640CrossRefGoogle Scholar
  10. Gibbons JG et al (2009) Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26:2731–2744CrossRefPubMedGoogle Scholar
  11. Grad YH et al (2012) Genomic epidemiology of the Escherichia coli O104: H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A 109:3065–3070CrossRefPubMedPubMedCentralGoogle Scholar
  12. Guffanti A et al (2009) A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 10:1CrossRefGoogle Scholar
  13. Horner DS et al (2010) Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform 11:181–197CrossRefPubMedGoogle Scholar
  14. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945CrossRefGoogle Scholar
  15. King JL et al (2014) High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet 12:128–135CrossRefPubMedGoogle Scholar
  16. Levin JZ et al (2009) Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol 10:1CrossRefGoogle Scholar
  17. Li R et al (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317CrossRefPubMedPubMedCentralGoogle Scholar
  18. Liu L et al (2012) Comparison of next-generation sequencing systems. Biomed Res Int 2012:251364Google Scholar
  19. Lo YD, Chiu RW (2009) Next-generation sequencing of plasma/serum DNA: an emerging research and molecular diagnostic tool. Clin Chem 55:607–608CrossRefPubMedGoogle Scholar
  20. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402CrossRefGoogle Scholar
  21. Margulies M et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380CrossRefPubMedPubMedCentralGoogle Scholar
  22. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682CrossRefPubMedGoogle Scholar
  23. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A 74:560–564CrossRefPubMedPubMedCentralGoogle Scholar
  24. Mcellistrem MC et al (2009) Genetic diversity of the pneumococcal capsule: implications for molecular-based serotyping. Future Microbiol 4:857–865CrossRefPubMedGoogle Scholar
  25. Mckernan KW et al (2011) Reagents, methods, and libraries for bead-based sequencing. Patent no. US20110077169 A1Google Scholar
  26. Medvedev P et al (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6:S13–S20CrossRefPubMedGoogle Scholar
  27. Metzker ML (2005) Emerging technologies in DNA sequencing. Genome Res 15:1767–1776CrossRefPubMedGoogle Scholar
  28. Miller JR et al (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327CrossRefPubMedPubMedCentralGoogle Scholar
  29. Qin J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65CrossRefPubMedPubMedCentralGoogle Scholar
  30. Ram JL et al (2011) Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform. Syst Biol Reprod Med 57:162–170CrossRefPubMedGoogle Scholar
  31. Reich D et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060CrossRefPubMedPubMedCentralGoogle Scholar
  32. Rohland N et al (2010) Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol 8:e1000564CrossRefPubMedPubMedCentralGoogle Scholar
  33. Sanger F et al (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467CrossRefPubMedPubMedCentralGoogle Scholar
  34. Schloss JA (2008) How to get genomes at one ten-thousandth the cost. Nat Biotechnol 26:1113CrossRefPubMedGoogle Scholar
  35. Scholz MB et al (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:9–15CrossRefPubMedGoogle Scholar
  36. Schuster SC (2007) Next-generation sequencing transforms today’s biology. Nature 200:16–18Google Scholar
  37. Silva Ascencio H (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43(2):109–116CrossRefGoogle Scholar
  38. Sultan M et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956–960CrossRefPubMedGoogle Scholar
  39. Taylor KH et al (2007) Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res 67:8511–8518CrossRefPubMedGoogle Scholar
  40. Turnbaugh PJ et al (2007) The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature 449:804CrossRefPubMedPubMedCentralGoogle Scholar
  41. Valouev A et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051–1063CrossRefPubMedPubMedCentralGoogle Scholar
  42. Van Dijk EL et al (2014) Ten years of next-generation sequencing technology. Trends Genet 30:418–426CrossRefPubMedGoogle Scholar
  43. Van Tassell CP et al (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247–252CrossRefPubMedGoogle Scholar
  44. Warnecke F et al (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565CrossRefPubMedGoogle Scholar
  45. Willner D et al (2011) Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A 108:4547–4553CrossRefPubMedGoogle Scholar
  46. Yang F et al (2012) Saliva microbiomes distinguish caries-active from healthy human populations. ISME J 6:1–10CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Satendra Singh
    • 1
  • Anjali Rao
    • 1
  • Pallavi Mishra
    • 1
  • Arvind Kumar Yadav
    • 1
  • Ranjeet Maurya
    • 1
  • Sukhdeep Kaur
    • 1
  • Gitanjali Tandon
    • 1
  1. 1.Department of Computational Biology and BioinformaticsJacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and SciencesAllahabadIndia

Personalised recommendations