Protein-based phylogenetic analysis by using hydropathy profile of amino acids

FEBS Letters

Volumn 580, Issue 22, 2006, Pages 5321-5327

  Liu, Na ^a   Wang, Tianming ^a,b  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b HAINAN NORMAL UNIVERSITY   (China)

Author keywords

Distance matrix; Hydropathy profile; LZ complexity; Protein feature sequences; Protein primary structures

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; HUMAN; NONHUMAN; PHYLOGENY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE;

AMINO ACIDS; ANIMALS; HUMANS; HYDROPHOBICITY; PHYLOGENY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 33748808998     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.08.086     Document Type: Article

References (21)

1. Komatsu K., Zhu S., Fushimi H., Qui T.K., Cai S., and Kadota S. Phylogenetic analysis based on 18S rRNA gene and matK gene sequences of Panax vietnamensis and five related species. Planta Med. 67 (2001) 461-465
2. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
3. Felsenstein J. Inferring phylogenies from protein sequences by parsimony, distance and likelihood methods. Meth. Enzymol. 266 (1996) 418-427
4. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 8 (2001) 754-755
5. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefing Bioinform. 5 2 (2004) 150-163
6. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
7. Snel B., Bork P., and Huynen M.A. Genome phylogeny based on gene content. Nat. Genet. 21 (1999) 108-110
8. Stuart G.W., Moffett K., and Leader J.J. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol. Biol. Evol. 19 (2002) 554-562
9. Li M., Badger J.H., Chen X., Kwong S., Kearney P., and Zhang H. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17 (2001) 149-154
10. Lolkema J.S., and Slotboom D.J. Hydropathy profile alignment: a tool to search for structural homologues of membrane proteins. FEMS Microbiol. Rev. 22 4 (1998) 305-322
11. Cobbe N., and Heck M.M.S. The evolution of SMC proteins: phylogenetic analysis and structural implications. Mol. Biol. Evol. 21 2 (2004) 332-347
12. Lempel A., and Ziv J. On the complexity of finite sequences. IEEE Trans. Inform. Theory 22 (1976) 75-81
13. Otu H.H., and Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19 (2003) 2122-2130
14. Felsenstein J. PHYLIP- phylogeny inference package (version 3.2). Cladistics 5 (1989) 164-166
15. Page R.D.M. TreeView: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12 4 (1996) 357-358
16. Cobbe N., and Heck M.M.S. Review: SMCs in the world of chromosome biology-from prokaryotes to higher eukaryotes. J. Struct. Biol. 129 (2000) 123-143
17. Soppa J. Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins. Gene 278 (2001) 253-264
18. Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5 (2004) 113-131
19. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31 13 (2003) 3497-3500
20. Horn F., Weare J., Beukers M.W., Hörsch S., Bairoch A., Chen W., Edvardsen Ø., Campagne F., and Vriend G. GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 26 1 (1998) 277-281
21. Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8 (1990) 52-56