Biomedical subjects

Laurent Guéguen

Publications and source records attributed to Laurent Guéguen.

3 recordsLinked to original sources

PubMed2006

UV-targeted dinucleotides are not depleted in light-exposed prokaryotic genomes.

We have investigated the hypothesis that pyrimidine dinucleotides are avoided in light-exposed genomes as the result of selective pressure due to high ultraviolet (UV) exposure. The main damage to DNA produced by UV radiation is known to be the formation of pyrimidine photoproducts: it is estimated that about 10 dimers per minute are formed in an Escherichia coli chromosome exposed to the UV light in direct overhead sunlight at sea level. It is also known that on an E. coli chromosome exposed to UVb wavelengths (290-320 nm), pyrimidine photoproducts are formed in the following proportions: 59% TpT, 7% CpC, and 34% CpT plus TpC. We have analyzed all available complete prokaryotic genomes and the model organism Prochlorococcus marinus and have found that pyrimidine dinucleotides are not systematically avoided. This suggests that prokaryotes must have sufficiently effective protection and repair systems for UV exposure to not affect their dinucleotide composition.

DNA Damage↗

PubMed2006

A computational prediction of isochores based on hidden Markov models.

Mammalian genomes are organised into a mosaic of regions (in general more than 300 kb in length), with differing, relatively homogeneous G+C contents. The G+C content is the basic characteristic of isochores, but they have also been associated with many other biological properties. For instance, the genes are more compact and their density is highest in G+C rich isochores. Various ways of locating isochores in the human genome have been developed, but such methods use only the base composition of the DNA sequences. The present paper proposes a new method, based on a hidden Markov model, which takes into account several of the biological properties associated with the isochore structure of a genome. This method leads to good segmentation of the human genome into isochores, and also permits a new analysis of the known heterogeneity of G+C rich isochores: most (60%) of the G+C poor genes embedded in G+C rich isochores have UTR sequences characteristic of G+C rich genes. This genomic feature is discussed in the context of both evolution and genome function.

5' Untranslated Regions↗

PubMed2005

Sarment: Python modules for HMM analysis and partitioning of sequences.

Sarment is a package of Python modules for easy building and manipulation of sequence segmentations. It provides efficient implementation of usual algorithms for hidden Markov Model computation, as well as for maximal predictive partitioning. Owing to its very large variety of criteria for computing segmentations, Sarment can handle many kinds of models. Because of object-oriented programming, the results of the segmentation are very easy tomanipulate.

Algorithms↗