Systematic Strategies

  • Saeid KadkhodaeiEmail author
  • Farahnaz Sadat Golestan Hashemi
  • Morvarid Akhavan Rezaei
  • Sahar Abbasiliasi
  • Joo Shun Tan
  • Hamid Rajabi Memari
  • Faruku Bande
  • Ali Baradaran
  • Mahdi Moradpour
  • Arbakariya B. Ariff
Part of the SpringerBriefs in Systems Biology book series (BRIEFSBIOSYS)


This section outlines efficient stepwise procedures for analyzing the matrix attachment regions (MARs), translation initiation sites (TIS), signal peptide (SP) sequences, gene optimization, and transformation systems. The strategies initially include data mining (DNA, RNA, and protein for MARs, TIS, and SP, respectively) and screening for the validated data. The in silico process for MARs exploration comprises motif search and comparison in databases, correlation analysis, design, and evaluation of an artificial MAR sequence. Investigation on TIS is carried out based on the statistical evaluation of the nucleotide occurrence variation around the ATG (translation initiation) site. Various programs are available to predict signal peptide sequences throughout the genome, among which SignalP is preferred in terms of performance comparing other similar programs. For gene optimization, in addition to codon preference, the mRNA secondary structures are also evaluated. Finally, the transformation procedures and efficiency of different methods are discussed.


S/MARs TIS SP Gene optimization 


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Copyright information

© The Author(s) 2018

Authors and Affiliations

  • Saeid Kadkhodaei
    • 1
    Email author
  • Farahnaz Sadat Golestan Hashemi
    • 2
  • Morvarid Akhavan Rezaei
    • 3
  • Sahar Abbasiliasi
    • 4
  • Joo Shun Tan
    • 5
  • Hamid Rajabi Memari
    • 6
  • Faruku Bande
    • 7
  • Ali Baradaran
    • 8
    • 9
  • Mahdi Moradpour
    • 10
  • Arbakariya B. Ariff
    • 11
  1. 1.Research Institute for Biotechnology and BioengineeringIsfahan University of TechnologyIsfahanIran
  2. 2.Plant Genetics, AgroBioChem Department, Gembloux Agro-Bio TechUniversity of LiègeLiègeBelgium
  3. 3.Tropical Infectious Diseases Research and Education Centre (TIDREC), Faculty of MedicineUniversity of MalayaKuala LumpurMalaysia
  4. 4.Halal Products Research InstituteUniversiti Putra MalaysiaSeri KembanganMalaysia
  5. 5.Bioprocess Technology, School of Industrial TechnologyUniversiti Sains MalaysiaGeorge Town, PenangMalaysia
  6. 6.SynHiTechThornhillCanada
  7. 7.Department of Veterinary Services, Ministry of Animal Health and Fisheries DevelopmentUsman Faruk Secretariat, SokotoSokotoNigeria
  8. 8.Mater ResearchTranslational Research InstituteWoolloongabbaAustralia
  9. 9.Faculty of Medicine, Translational Research Institute, Diamantina InstituteUniversity of QueenslandBrisbaneAustralia
  10. 10.Institute of plantation studiesUniversiti Putra MalaysiaSeri KembanganMalaysia
  11. 11.Faculty of Biotechnology and Biomolecular SciencesUniversiti Putra MalaysiaSeri KembanganMalaysia

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