Analysis of Protean Genomics to Increase Genome Annotation Accuracy

  • Lina Zhao
  • Baoling He
  • Weiwei Li
  • Candong Wei
Conference paper
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 217)


Advances in sequencing strategies facilitate complete genomic sequence of a variety of organisms. However, conventional computational predictions for genome annotation remain imperfect. Here, we applied a protean genomics approach to complement genome annotation by combining bioinformatics analysis and proteomic data. By using Shebelle Flexner 2a as a model, a total of 1041 proteins were unambiguously assigned, including 240 hypothetical proteins. Through comprehensive analysis against in-house N-terminal extension database, three annotated open reading frames (Offs) were respectively extended upstream. Above all, eight new ORFs were discovered by searching our MS/MS data against all six possible reading frames of S. Flexner 2a str. 301 genome, which were not predicted by any other annotation approaches. Our findings indicate that protean genomic analysis is quite qualified for comprehensive and accurate genome-wide annotation. This strategy could be taken as a routine work.


Genome annotation Protean genomics Shebelle flexner 


  1. 1.
    Nielsen P, Krogh A (2005) Large-scale prokaryotic gene prediction and comparison to genome annotation. Biotin Fermatas 1(24):4322–4329Google Scholar
  2. 2.
    Venter E, Smith RD, Pane SH (2011) Protean genomic analysis of bacteria and archaic: a 46 organism case study. Plops One 2(11):587–591Google Scholar
  3. 3.
    Paullina A, Harrington ED, Bork P (2008) Large gene overlaps in prokaryotic genomes: result of functional constraints or miss predictions? BMC Genomics 3(9):335–338Google Scholar
  4. 4.
    Reuse S, Chairlady R, Pander A (2011) Protean genomics. Proteomics 4(11):620–630Google Scholar
  5. 5.
    Joseph A, Guyana M, Jean A (2012) High-throughput protean genomics of ruggeri poverty: seeding a better genomic annotation for the whole marine rose obiter clad. BMC Genomics 5(13):73–77Google Scholar
  6. 6.
    Scrawl MM, Sigel TK, Salomon DR (2010) Functional port ergonomics-embracing complexity. Semen Immune 6(23):235–251Google Scholar
  7. 7.
    Armin gaud J (2010) Prot ergonomics and systems biology: quest for the ultimate missing parts expert rev. Proteomics 7(5):72–77Google Scholar
  8. 8.
    Payne SH, Huang ST, Pieper R (2010) A port ergonomic update to Yesinia: enhancing genome annotation. BMC Genomics 8(11):460–465Google Scholar
  9. 9.
    Van Boggle RA, Schiller EE, Thomas JD, Leichardt FC (1999) Diagnosis of cellular states of microbial organisms using proteomics. Electro Pharoses 9(11):2149–2159Google Scholar
  10. 10.
    Anson C, Purina SO, Adkins JN, Lipton MS, Smith RD (2008) Prot ergonomics: needs and roles to be filled by proteomics in genome annotation. Brief Font Genomics Proteomics 10(7):50–62CrossRefGoogle Scholar
  11. 11.
    Al-Hisami K, Raja Kumar K, Bulloch D, Robins-Browne R (2001) Genetic organization of the she pathogen city island in Shebelle Flexner 2a. Microbe Pathos 11(3):1–8Google Scholar
  12. 12.
    Sewers RG (2005) Transcript analysis of Escherichia coli K-12 insertion element IS5. FEMS Microbiol Lett 12(24):397–401CrossRefGoogle Scholar
  13. 13.
    Alex E, Blanc-Petard AB (2009) Hydrophobic peptides: novel regulators within bacterial membrane. Mol Microbiol 13(72):5–11Google Scholar
  14. 14.
    Kumar A (2009) An overview of nested genes in eukaryotic genomes. Eukaryot Cell 14(8):1321–1329CrossRefGoogle Scholar
  15. 15.
    Jab worksite DM, Beam-Miller M, Lure G, Barents-Reynolds R (2007) Potential regulatory relationship between the nested gene DDC8 and its host gene tissue inhibitor of metalloproteinase-2. Physiol Genomics 15(28):168–178Google Scholar

Copyright information

© Springer-Verlag London 2013

Authors and Affiliations

  1. 1.College of Life SciencesHubei United UniversityTangshanChina
  2. 2.Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

Personalised recommendations