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We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction(More)
In this paper, we describe the basis of EuGène, a gene finder for eucaryotic organisms applied to Arabidopsis thaliana. The specificity of EuGène, compared to existing gene finding software, is that EuGène has been designed to combine the output of several information sources, including output of other software or user information. To achieve this, a(More)
EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. EUGENE'HOM is able to take into account multiple homologous sequences from more or less closely related organisms. It integrates the results of TBLASTX analysis, splice site and start codon prediction and a robust coding/non-coding probabilistic model which(More)
BACKGROUND Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs. RESULTS Using a combination of in silico and experimental approaches, we identified and characterized(More)
Changes to mRNA lifetime adjust mRNA concentration, facilitating the adaptation of growth rate to changes in growth conditions. However, the mechanisms regulating mRNA lifetime are poorly understood at the genome-wide scale and have not been investigated in bacteria growing at different rates. We used linear covariance models and the best model selected(More)
EuGène, a gene finder for Arabidopsis thaliana, combines the output of several information sources, including output of other software or user information. To achieve this, a weighted DAG is built in such a way that a shortest feasible path in this graph represents the most likely gene structure of the underlying DNA sequence. The usual simple Bellman(More)
34392 Montpellier cedex 5 RÉ SUMÉ. Le but essentiel de nombreuses expériences effectuées en biologie moléculaire est d'accumuler, au moindre effort, suffisamment d'informations sur un objet pour déterminer de façon non ambiguë ses caractéristiques d'intérêt biologique. Très souvent, les données obtenues a ` la suite d'une série d'expériences forment un(More)
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