Join for Free!
122512 members

table of contents table of contents

In general, the construction of trees is based on sequence alignments. This …

Home » Biology Articles » Methods & Techniques » Comparing sequences without using alignments: application to HIV/SIV subtyping » References

- Comparing sequences without using alignments: application to HIV/SIV subtyping

  1. Lee C, Grasso C, Sharlow MF: Multiple sequence alignment using partial order graphs.

    Bioinformatics 2002, 18:452-464. 

  2. Grasso C, Lee C: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems.

    Bioinformatics 2004, 20:1546-1556. 

  3. Raphael B, Zhi D, Tang H, Pevzner P: A novel method for multiple alignment of sequences with repeated and shuffled elements.

    Genome Res 2004, 14:2336-2346.

  4. Laprevotte I, Brouillet S, Terzian C, Hénaut A: Retroviral oligonucleotide distributions correlate with biased nucleotide compositions of retrovirus sequences, suggesting a duplicative stepwise molecular evolution.

    J Mol Evol 1997, 44:214-225. 

  5. Laprevotte I, Pupin M, Coward E, Didier G, Terzian C, Devauchelle C, Hénaut A: HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, «retroviral signatures» of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution.

    Mol Biol Evol 2001, 18:1231-1245. 

  6. Karlin S, Ladunga I: Comparisons of eukaryotic genomic sequences.

    Proc Natl Acad Sci USA 1994, 91:12832-12836. 

  7. Didier G: Caractérisation des N-écritures et application à l'étude des suites de complexité ultimement n + cste.

    Theor Comput Sc 1999, 215:31-49. 

  8. Didier G, Laprevotte I, Pupin M, Hénaut A: Local decoding of sequences and alignment-free comparison.

    J Comput Biol 2006, 13:1465-1476.

  9. Foley BT: An overview of the molecular phylogeny of lentiviruses. [http://www.hiv.lanl.gov/content/hiv-db/REVIEWS/reviews.html] 

  10. Kuiken CL, Leitner T: HIV-1 Subtyping. In Computational and Evolutionary Analysis of HIV Molecular Sequences. Edited by: Rodrigo AG, Learn GH. Jr. Kluwer Academic Publishers; 2001:27-53.

  11. Robertson DL, Anderson JP, Bradac JA, Carr JK, Foley B, Funkhouser RK, Gao F, Hahn BH, Kalish ML, Kuiken C, Learn GH, Leitner T, McCutchan F, Osmanov S, Peeters M, Pieniazek D, Salminen M, Sharp PM, Wolinsky S, Korber B: HIV-1 Nomenclature Proposal (a reference guide to HIV-1 classification). [http://www.hiv.lanl.gov/content/hiv-db/REVIEWS/reviews.html] 

  12. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins LB, Arthur LO, Peeters M, Shaw GM, Sharp PM, Hahn BH: Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes.

    Nature 1999, 397:436-441.

  13. Leitner T, Foley B, Hahn B, Marx P, McCutchan F, Mellors J, Wolinsky S, Korber B (Eds): HIV Sequence Compendium

    In Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, LA-URnumber 04-7420 2003.

  14. Peeters M: Recombinant HIV Sequences: Their Role in the Global Epidemic. [http://www.hiv.lanl.gov/content/hiv-db/REVIEWS/reviews.html] 

  15. Beer BE, Bailes E, Sharp PM, Hirsch VM: Diversity and Evolution of Primate Lentiviruses. [http://www.hiv.lanl.gov/content/hiv-db/REVIEWS/reviews.html

  16. Comparing sequences without using alignment scores [http://iml.univ-mrs.fr/~didier/laprevot/] 

  17. HIV-1/HIV-2/SIV Complete Genomes [http://www.hiv.lanl.gov/content/hiv-db/COMPENDIUM/2000/HIV12SIVcomplete.pdf] 

  18. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

    Nucleic Acids Res 1994, 22:4673-4680.

  19. Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.

    Bioinformatics 1999, 15:211-218. 

  20. Eddy SR: Profile Hidden Markov Models.

    Bioinformatics 1998, 14:755-763. 

  21. HMMER [http://hmmer.janelia.org/] 

  22. The 2000 HIV Sequence Compendium [http://www.hiv.lanl.gov/content/hiv-db/HTML/compendium.html] 

  23. HIV-1 Nomenclature Proposal [http://hiv-web.lanl.gov/content/hiv-db/REVIEWS/nomenclature/Nomen.html] 

  24. Los Alamos HIV sequence database [http://hiv-web.lanl.gov/] 

  25. Felsenstein J: PHYLIP (Phylogeny Inference Package) version 3.6. In Distributed by the author. Department of Genome Sciences. University of Washington, Seattle; 2005. 

  26. Felsenstein J: Confidence intervals on phylogenies: an approach using the bootstrap.

    Evolution 1985, 39:783-791. 

rating: 0.00 from 0 votes | updated on: 12 Aug 2009 | views: 9691 |

Rate article: