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

Abstract : 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 user-specified 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 non-coding 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.
Type de document :
Article dans une revue
BMC Bioinformatics, BioMed Central, 2007, 8 (1), 〈10.1186/1471-2105-8-1〉
Liste complète des métadonnées

https://hal.inria.fr/inria-00289069
Contributeur : Maude Pupin <>
Soumis le : jeudi 19 juin 2008 - 14:43:17
Dernière modification le : jeudi 18 janvier 2018 - 01:35:42

Lien texte intégral

Identifiants

Collections

Citation

Gilles Didier, Laurent Debomy, Maude Pupin, Ming Zhang, Alexander Grossmann, et al.. Comparing sequences without using alignments: application to HIV/SIV subtyping. BMC Bioinformatics, BioMed Central, 2007, 8 (1), 〈10.1186/1471-2105-8-1〉. 〈inria-00289069〉

Partager

Métriques

Consultations de la notice

207