162
Views
2
CrossRef citations to date
0
Altmetric
Articles

An efficient method for measuring the similarity of protein sequences

&
Pages 363-370 | Received 28 Feb 2016, Accepted 01 Apr 2016, Published online: 22 Apr 2016

References

  • S.B. Needleman and C.D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol. 48 (1970), pp. 443–453.
  • H.H. Otu and K. Sayood, A new sequence distance measure for phylogenetic tree construction, Bioinformatics 19 (2003), pp. 2122–2130.
  • S. Vinga and J. Almeida, Alignment-free sequence comparison - A review, Bioinformatics 19 (2003), pp. 513–523.
  • M. Randic, J. Zupan, A.T. Balaban, D. Vikic-Topic, and D. Plavsic, Graphical representation of proteins, Chem. Rev. 111 (2011), pp. 790–862.
  • M. Randic, M. Novic, and D. Plavsic, Milestones in graphical bioinformatics, Int. J. Quantum Chem. 113 (2013), pp. 2413–2446.
  • E. Hamori and J. Ruskin, H-curves, a novel method of representation of nucleotide series especially suited for long DNA sequences, J. Biol. Chem. 258 (1983), pp. 1318–1327.
  • M. Randic, M. Novic, and M. Vracko, On novel representation of proteins based on amino acid adjacency matrix, SAR QSAR Environ. Res. 19 (2008), pp. 339–349.
  • M. Randic, Very efficient search for protein alignment - VESPA, J. comput. Chem. 33 (2012), pp. 702–707.
  • P. He, D. Li, Y. Zhang, X. Wang, and Y. Yao, A 3D graphical representation of protein sequences based on the Gray code, J. Theor. Biol. 304 (2012), pp. 81–87.
  • H. Yu and D. Huang, Normalized feature vectors: A novel alignment-free sequence comparison method based on the numbers of adjacent amino acid, IEEE trans. Comput. Biol. Bioinf. 10 (2013), pp. 457–467.
  • Y. Yao, Q. Dai, C. Li, P. He, X. Nan, and Y. Zhang, Analysis of similarity/dissimilarity of protein sequences, proteins 73 (2008), pp. 864–871.
  • P. He, Y. Zhang, Y. Yao, Y. Tang, and X. Nan, The graphical representation of protein sequences based on the physicochemical properties and its applications, J. Compu. Chem. 31 (2010), pp. 2136–2142.
  • Z. Wu, X. Xiao, and K. Chou, 2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids, J. Theor. Biol. 267 (2010), pp. 29–34.
  • P. He, X. Li, J. Yang, and J. Wang, A novel descriptor for protein similarity analysis, MATCH Commun. Math. Comput. Chem. 65 (2011), pp. 445–458.
  • P. He, D. Li, Y. Zhang, X. Wang, and Y. Yao, A novel graphical representation of proteins and its application, Physica A. 391 (2012), pp. 93–99.
  • M.J. Ford, Molecular evolution of transferrin: Evidence for positive selection in salmonids, Mol. Biol. Evol. 18 (2001), pp. 639–647.
  • I. Ultisky, D. Burnstein, T. Tuller, and B. Chor, The average common substring approach to phylogenomic reconstruction, J. Comput. Biol. 13 (2006), pp. 336–350.
  • G. Chang and T. Wang, Phylogenetic analysis of protein sequences based on distribution of length about common substring, Protein J. 30 (2011), pp. 167–172.
  • Y. Yao, F. Kong, Q. Dai, and P. He, A sequence-segmented method applied to the similarity analysis of long protein sequence, MATCH Commun. Math. Comput. Chem. 70 (2013), pp. 431–450.
  • C.Z. Guo and M.Q. Sun, ClustalW – A software for multiple sequence alignment of protein and nucleic acid sequence, Lett. Biotech. 11 (2000), pp. 146–149.
  • A. El-Lakkani and H. Mahran, An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical representation, SAR QSAR Environ. Res. 26 (2015), pp. 125–137.
  • A. El-Lakkani and S. EL-Sherif, Similarity analysis of protein sequences based on 2D and 3D amino acid adjacency matrices, Chem. Phys. Lett. 590 (2013), pp. 192–195.
  • N. Jafarzadeh and A. Iranmanesh, A new measure for pairwise comparison of protein sequences, MATCH Commun. Math. Comput. Chem. 74 (2015), pp. 563–574.
  • T. Ohlson and A. Elofsson, Profnet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins, BMC Bioinformatics. 6 (2005), pp. 253–261.
  • T. Ohlson, The use of evolutionary information in protein alignments and homology identification, Doctoral thesis, Stockholm Bioinformatics Centre, Stockholm University, Sweden, 2007.
  • M. Mindaugas and C. Venclovas, Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison, BMC Bioinformatics 11 (2010), pp. 89–92.
  • P.R. Fleming, M.D, Milne, D.G. Morgan, and M. Morris, A statistical analysis of amino acid sequence in protein chains, Bio-Med. Comput. 3 (1972), pp. 91–100.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.