Biomedical subjects

Ivan Laprevotte

Publications and source records attributed to Ivan Laprevotte.

3 recordsLinked to original sources

PubMed2007

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

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.

Animals↗

PubMed2006

Local decoding of sequences and alignment-free comparison.

Subword composition plays an important role in a lot of analyses of sequences. Here we define and study the "local decoding of order N of sequences," an alternative that avoids some drawbacks of "subwords of length N" approaches while keeping informations about environments of length N in the sequences ("decoding" is taken here in the sense of hidden Markov modeling, i.e., associating some state to all positions of the sequence). We present an algorithm for computing the local decoding of order N of a given set of sequences. Its complexity is linear in the total length of the set (whatever the order N) both in time and memory space. In order to show a use of local decoding, we propose a very basic dissimilarity measure between sequences which can be computed both from local decoding of order N and composition in subwords of length N. The accuracies of these two dissimilarities are evaluated, over several datasets, by computing their linear correlations with a reference alignment-based distance. These accuracies are also compared to the one obtained from another recent alignment-free comparison.

Computational Biology↗

PubMed2003

The new variant of the Creutzfeldt-Jakob disease accounts for no relative increase of the Creutzfeldt-Jakob disease mortality rate in the United Kingdom; this fits ill with the new variant being the consequence of consumption of food infected with the agent of Bovine Spongiform Encephalopathy.

BACKGROUND: A new variant of Creutzfeldt-Jakob disease was described in the United Kingdom. It is often claimed that it is caused by consumption of food infected with the agent of bovine spongiform encephalopathy. However, this remains open to question because the number of cases of the variant is, at the present time, less than would be expected from a major food-borne source. DISCUSSION: The EUROCJD cooperative study presents currently available epidemiological data of Creutzfeldt-Jakob disease and its new variant, for nine European countries plus Australia and Canada. Unexpectedly, for the United Kingdom where all but a few cases of the new variant have been reported, these cases have to be included in the incidence curve of the sporadic forms of the disease in order to obtain the best fit with the median curve from all the countries. This variant could be merely a rare clinical phenotype within the sporadic disease. The published clinical and experimental data which suggest that it is linked with bovine spongiform encephalopathy, lead us to propose that this link could be a common etiological origin other than consumption of bovine infected food. In any case, public health recommendations hold and further investigation is required. SUMMARY: The lack of a relative increase of the Creutzfeldt-Jakob-disease mortality rate in the United Kingdom, does not fit well with the new variant being the consequence of consumption of food infected with the agent of bovine spongiform encephalopthy.

Animals↗