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

Didier, Gilles; Debomy, Laurent; Pupin, Maude; Zhang, Ming; Grossmann, Alexander; Devauchelle, Claudine; Laprevotte, Ivan

doi:10.1186/1471-2105-8-1

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

Journal Article · Tue Jan 02 00:00:00 EST 2007 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-8-1· OSTI ID:1626333

Didier, Gilles ^[1]; Debomy, Laurent ^[2]; Pupin, Maude ^[2]; Zhang, Ming ^[3]; Grossmann, Alexander ^[4]; Devauchelle, Claudine ^[4]; Laprevotte, Ivan ^[4]

Unite Mixte de Recherche (UMR), Marseille Cedex (France). Centre National de la Recherche Scientifique (CNRS). Inst. Mathematique de Luminy
Laboratoire d'Informatique Fondamentale de Lille (LIFL), Villeneuve d'Ascq (France). Equipe Bioinfo
Gottingen Univ. (Germany). Inst. of Microbiology and Genetics. Dept. of Bioinformatics; Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Biology and Biophysics Group
Unite Mixte de Recherche (UMR), Evry (France). Centre National de la Recherche Scientifique (CNRS). Lab. Statistique et Genome

Background: In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment. Results: In this paper, HIV (Human Immunodeficiency Virus) and SIV (Simian Immunodeficiency Virus) sequence data are used to evaluate this method. The program produces tree topologies that are identical to those obtained by a combination of standard methods detailed in the HIV Sequence Compendium. Manual alignment editing is not necessary at any stage. Furthermore, only one userspecified parameter is needed for constructing trees. Conclusion: The extensive tests on HIV/SIV subtyping showed that the virus classifications produced by our method are in good agreement with our best taxonomic knowledge, even in noncoding LTR (Long Terminal Repeat) regions that are not tractable by regular alignment methods due to frequent duplications/insertions/deletions. Our method, however, is not limited to the HIV/ SIV subtyping. It provides an alternative tree construction without a time-consuming aligning procedure.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1626333

Journal Information:: BMC Bioinformatics, Vol. 8, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Identifying protein complexes based on an edge weight algorithm and core-attachment structure Wang, Rongquan; Liu, Guixia; Wang, Caixia BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3007-y	journal	September 2019
Estimating linkage disequilibrium from genotypes under Hardy-Weinberg equilibrium Hui, Tin-Yu J.; Burt, Austin BMC Genetics, Vol. 21, Issue 1 https://doi.org/10.1186/s12863-020-0818-9	journal	February 2020
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