Biomedical subjects

Maude Pupin

Publications and source records attributed to Maude Pupin.

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

A revised annotation and comparative analysis of Helicobacter pylori genomes.

Huge amounts of genomic information are currently being generated. Therefore, biologists require structured, exhaustive and comparative databases. The PyloriGene database (http://genolist.pasteur.fr/PyloriGene) was developed to respond to these needs, by integrating and connecting the information generated during the sequencing of two distinct strains of Helicobacter pylori. This led to the need for a general annotation consensus, as the physical and functional annotations of the two strains differed significantly in some cases. A revised functional classification system was created to accommodate the existing data and to make it possible to classify coding sequences (CDS) into several functional categories to harmonize CDS classification. The annotation of the two complete genomes was revised in the light of new data, allowing us to reduce the percentage of hypothetical proteins from approximately 40 to 33%. This resulted in the reassignment of functions for 108 CDS (approximately 7% of all CDS). Interestingly, the functions of only approximately 13% of CDS (222 out of 1658 CDS) were annotated as a result of work done directly on H.pylori genes. Finally, comparison of the two published genomes revealed a significant amount of size variation between corresponding (orthologous) CDS. Most of these size variations were due to natural polymorphisms, although other sources of variation were identified, such as pseudogenes, new genes potentially regulated by slipped-strand mispairing mechanism, or frame-shifts. 113 of these differences were due to different start codon assignments, a common problem when constructing physical annotations.

Databases, Nucleic Acid↗