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


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

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

The N-local-decoding method has shown its satisfactory applications in HIV/SIV subtyping. The deduced classifications are in good agreement with our best taxonomic knowledge, even for non-coding LTR regions that are not tractable by regular alignment methods due to frequent duplications/insertions/deletions. However, its application is not limited in HIV/SIV subtyping. In general, the advantages of this method are:

1) It generates sequence dissimilarity matrices without requiring sequence alignments.

2) It has only one user-specified parameter (N: the order of the site neighborhoods).

3) It is fast.

Thus the N-local-decoding method provides a promising approach to the rapid construction of trees without a time-consuming step of aligning sequences.


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