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Y Quentin

Publications and source records attributed to Y Quentin.

13 recordsLinked to original sources
PubMed1995

A frameshift error detection algorithm for DNA sequencing projects.

During the determination of DNA sequences, frameshift errors are not the most frequent but they are the most bothersome as they corrupt the amino acid sequence over several residues. Detection of such errors by sequence alignment is only possible when related sequences are found in the databases. To avoid this limitation, we have developed a new tool based on the distribution of non-overlapping 3-tuples or 6-tuples in the three frames of an ORF. The method relies upon the result of a correspondence analysis. It has been extensively tested on Bacillus subtilis and Saccharomyces cerevisiae sequences and has also been examined with human sequences. The results indicate that it can detect frameshift errors affecting as few as 20 bp with a low rate of false positives (no more than 1.0/1000 bp scanned). The proposed algorithm can be used to scan a large collection of data, but it is mainly intended for laboratory practice as a tool for checking the quality of the sequences produced during a sequencing project.

Algorithms↗
PubMed1995

Analysis of errors in finished DNA sequences: the surfactin operon of Bacillus subtilis as an example.

Increased productivity in DNA sequencing would not be valid without a straightforward detection and estimation of errors in finished sequences. The sequence of the surfactin operon from Bacillus subtilis was obtained by two different groups and by chance we were also working on the same chromosome region. Taking advantage of this situation we report in this paper, the number and nature of errors found in the overlapping part of the DNA sequences obtained by the three laboratories. The coincidence of some of the errors with compression in sequence ladders and with secondary DNA structures as well as the detection of frameshift errors using computer programs, are demonstrated. Finally we discuss the definition of a new sequencing strategy that might minimize both the error rate and the cost of sequencing.

Artifacts↗
PubMed1994

A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes.

The question of the origin of the B1 family of rodents is addressed. The modern B1 elements are similar to the left Alu monomer, but with a 9 bp deletion and a 29 bp duplication. Search of databases for B1 elements that do not exhibit those modern features revealed sequence fragments that are very similar to the free left Alu monomers (FLAMs) described in the primate genomes. In addition, the analysis reveals elements that have 10 bp or 7 bp deletion in place of the 9 bp deletion but without the 29 bp tandem duplication. The elements described define families of proto B1 elements (referred as PB1, PB1D10 and PB1D7) that appeared before the first modern B1 element. A phylogenetic reconstruction suggest that the origin of Alu and B1 families took place before the divergence between the primate and the rodent lineages and that each family has followed different evolutionary routes since this radiation.

Animals↗
PubMed1994

Fast identification of repetitive elements in biological sequences.

We have developed a fast filtering method for searching repetitive sequences in databases that allows the simultaneous identification of different families of repetitive elements during the same scanning. It discriminates between repetitive elements and non-related sequences by comparing the frequencies of k-words found in both groups of sequences. The distance used to sort out the sequences is based on a weighting of the k-words, which is obtained by performing a correspondence analysis on learning sets of correctly chosen sequences. The identification of Alu elements in human sequences is given as an illustration of the method. The Alu sequences are divided in four distinct groups of elements: the left and right monomers located on the direct and on the complementary strands. The results obtained on the test sets show that a very good discrimination is achieved with a word length of 6 b.p. Indeed, only 0.5% of the non-Alu sequences were incorrectly predicted as Alu elements for a threshold value allowing the identification of all Alu monomers. The misclassification of the different Alu monomers (1.4%) in the four groups of examples occurs only when the left and the right monomers are in the same orientation. Moreover, during the scanning of 63 GenBank sequences longer than 10 Kb, all the Alu elements were correctly identified (616 elements) and only a few non-Alu sequences were wrongly predicted as Alu elements (22 fragments). There is a real need for this kind of method since most of the repetitive elements are not annotated in the database entries. This method can then be used for a systematic screening of new sequences before their insertion in databases. It can also allow the creation of specific databases devoted to repetitive elements, which is a required step for any further analysis of those elements.

Algorithms↗
PubMed1994

Emergence of master sequences in families of retroposons derived from 7sl RNA.

The past few years have brought new insight into the evolution of families of retroposons. These are composed of a very small number of master sequences able to duplicate, and a large majority of copies that are inactive for retroposition. During the course of time, successive replacements of master sequences have produced waves of amplification that are recognizable as subfamilies. In the Alu and the B1 families, one can distinguish two evolutionary periods. The first involves only monomeric elements that are now extinguished (fossil elements) and is characterized by deep remodeling of the sequences. This period ends, in primates, with the fusion of a free left and a free right Alu monomer, producing the first modern Alu dimeric element; in rodents it ends with a tandem duplication of 29 bp to create the first modern B1 element. The second period is characterized by a great stability of the master sequences. The observed turn-over of master sequences is still an enigma. However, analysis of the contemporary master sequences and of the oldest master sequences provide some clues. Here, we review the very first stages of the appearance of the Alu and the B1 families in mammalian genomes.

Animals↗
PubMed1992

Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements.

The Alu dimeric elements are a common feature of the primate genomes, where they constitute a family of related sequences (1). The identification of a free left Alu monomer (FLAM) family plus a free right Alu monomer (FRAM) family suggests that the dimeric structure results from the fusion of a FLAM sequence with a FRAM sequence (2). Here, we describe a very old Alu-like monomeric family, referred to as FAM for fossil Alu monomer. This family arose from a 7SL RNA sequence and gave birth to the FLAM and FRAM families. From the results obtained, the evolution of the Alu family can be subdivided into two phases. The first phase, which involves only monomeric elements, is characterized by deep remodelling of the progenitor sequences and ends with the appearance of the first Alu dimeric element through the fusion of a FLAM and a FRAM element. The second phase, still in progress, starts with the first Alu dimeric element. This phase is characterized by the stabilization of the progenitor sequences.

Base Sequence↗
PubMed1992

Fusion of a free left Alu monomer and a free right Alu monomer at the origin of the Alu family in the primate genomes.

In the primate genome, a typical Alu element corresponds to a dimeric structure composed of two different but related monomeric sequences arranged in tandem. However, the analysis of primate sequences found in GenBank reveals the presence of free left and free right Alu elements. Here, we report the statistical study of those monomeric elements. We found that only a small fraction of them results from a deletion of a dimeric Alu sequence. The majority derives from the amplification of monomeric progenitor sequences and constitutes two families of monomeric elements: a family of free left Alu monomers that is composed of two subfamilies and a small family of free right Alu monomers. Both families predated the dimeric Alu elements, and a phylogenetic analysis strongly suggests that the first progenitor of the dimeric Alu family arose through the fusion of a free left monomer with a free right monomer.

Animals↗
PubMed1989

Successive waves of fixation of B1 variants in rodent lineage history.

A new method of analyzing phylogenetic relations among members of sequence family (Quentin 1988) discriminates at least six possible B1 subfamilies in the mouse genome. Several additional and independent observations suggest that these groupings have evolutionary significance, and that successive waves of fixation of new variants occur during rodent lineage history. We have reason to believe that, in a genome, the founder sequences of different families of retroposons are in competition with regard to the amplification/fixation process.

Animals↗
PubMed1988

The Alu family developed through successive waves of fixation closely connected with primate lineage history.

A new method of analyzing phylogenetic relations among members of the sequence family is presented and applied to human Alu sequences upon which work has been published. This method, based upon a correspondence analysis, works with large samples and yields easily interpretable graphical representations. Results obtained argue in favor of a new evolutionary scheme for Alu sequences, implying successive waves of amplification/fixation closely connected to primate lineage history.

Animals↗
PubMed1988

[Role of arteriography and x-ray computed tomography in the current evaluation of pigmented villonodular synovitis].

The angiographic characteristics of five surgically proven cases of pigmented villonodular synovitis are reported. A CT scan was performed in one case. CT scan arthrography is very useful when it demonstrates regions of high attenuation. The angiography never demonstrated in the five cases capillary blush nor arteriovenous shunting, but a regular hypervascular mass. These findings are helpful for the surgeon suggesting the best surgical approach and the best site of biopsy.

Adolescent↗
PubMed1987

[The course of a case of Maffucci's syndrome].

The syndrome of Maffucci is characterized by angioma association of the enchondromatose. It is a relatively rare syndrome. The lesions are evolutived. The treatment is surgical. His pronostic is marqued by high percentage of malign degenerescence.

Enchondromatosis↗
PubMedDate not supplied

[Bony metastases of the fingers. Apropos of 3 cases. Review of the literature].

Bone metastases of fingers are rare, are of highest incidence in men 40 to 60 years, and may reveal the presence of a primary cancer. Radiologic imaging shows almost constant osteolytic lesions, the primary usually being located in the bronchi. Short-term prognosis is poor, with a mean survival of three and a half months. Bone biopsy should be conducted routinely to determine nature of lesion in fingers.

Aged↗