The phylogeny of orthoretroviral long terminal repeats (LTRs)

Gene

Volumn 448, Issue 2, 2009, Pages 134-138

  Benachenhou, Farid ^a   Blikstad, Vidar ^a   Blomberg, Jonas ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Endogenous retrovirus; Hidden Markov Model; LTR; Phylogeny

Indexed keywords

NUCLEIC ACID; POL PROTEIN;

ARTICLE; CONTROLLED STUDY; HUMAN IMMUNODEFICIENCY VIRUS; LENTIVIRINAE; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MURINE LEUKEMIA VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHORETROVIRUS; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROVIRUS; RETROVIRUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; VIRUS STRAIN;

ANIMALS; CLUSTER ANALYSIS; ENDOGENOUS RETROVIRUSES; EVOLUTION, MOLECULAR; HUMANS; MARKOV CHAINS; MICE; PHYLOGENY; TERMINAL REPEAT SEQUENCES;

HUMAN ENDOGENOUS RETROVIRUSES; MOUSE MAMMARY TUMOR VIRUS; MURINE LEUKEMIA VIRUS;

EID: 70350247882     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.07.002     Document Type: Article

References (19)

1. Benachenhou F., et al. Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data. PLoS ONE 4 (2009) e5179
2. Blikstad V., Benachenhou F., Sperber G.O., and Blomberg J. Endogenous retroviruses: Evolution of human endogenous retroviral sequences: a conceptual account. Cell. Mol. Life. Sci. 65 (2008) 3348-3365
3. Blomberg J., Benachenhou F., Blikstad V., Sperber G., and Mayer J. Classification and nomenclature of endogenous retroviral sequences (ERVs), problems and recommendations. Gene (2009) PMID 19540319
4. Brand M. Structure learning in conditional probability models via an entropic prior and parameter extinction. Neural. Comp. 11 (1999) 1155-1182
5. Eddy S.R. Multiple alignment using hidden Markov models. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3 (1995) 114-120
6. Edgar R.C., and Sjolander K. Simultaneous sequence alignment and tree construction using hidden Markov models. Pac. Symp. Biocomput. (2003) 180-191
7. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22 (1988) 521-565
8. Gifford R.J., Katzourakis A., Tristem M., Pybus O.G., Winters M., and Shafer R.W. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 20362-20367
9. Jern P., and Coffin J.M. Effects of retroviruses on host genome function. Annu. Rev. Genet. 42 (2008) 709-732
10. Jern P., Sperber G.O., and Blomberg J. Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2 (2005) 50
11. Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., and Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110 (2005) 462-467
12. Karplus K., Karchin R., Shackelford G., and Hughey R. Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics 21 (2005) 4107-4115
13. Lavie L., Medstrand P., Schempp W., Meese E., and Mayer J. Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. J. Virol. 78 (2004) 8788-8798
14. Mager D.L., and Medstrand P. Retroviral repeat sequences. D, C. (D, C.)D, C.s), Nature Encyclopedia of the Human Genome (2003), Nature publishing group, London, UK
15. Rabiner L.A. tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77 (1989) 257-286
16. Sperber, G., Lövgren, A., Eriksson, N.-E., Benachenhou, F., Blomberg, J, 2009. RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences. BMC Bioinformatics 10, Suppl 6:S4. PMID 19534753.
17. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
18. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic. Acids Res. 22 (1994) 4673-4680
19. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic. Acids Res. 25 (1997) 4876-4882