A probabilistic algorithm for interactive huge genome comparison

Courtois, Pascal R.R.; Moncany, Maurice L. J.

doi:10.1093/bioinformatics/11.6.657

Cited by 2 publications

(6 citation statements)

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“…The use of the PAGEC program, which we have described previously (Courtois and Moncany 1995), allowed rapid comparison between the different genomes. Its flexibility made different types of comparison possible, from cross-comparison of huge genomes to strain-to-strain comparison.…”

Section: Resultsmentioning

confidence: 99%

“…The PAGEC probabilistic algorithm based on the creation of index tables and large key determination was tested on large genomes as previously described (Courtois and Moncany 1995). The comparison utilizes four parameters which can vary as a function of the length of the compared genomes and the homology rate.…”

Section: Methodsmentioning

confidence: 99%

“…The two first parameters affect the quality of the data defined by the difference between the theoretical vs the practical results. They were estimated by mathematical calculations and determined by experimentations as reported in the article in which we detailed PAGEC (Courtois and Moncany 1995). In this work, the four parameters were set at 3, 8, 3 and 25.…”

Section: Methodsmentioning

confidence: 99%

“…However, these methods are not only time and memory consuming but also limited in their range of applications, particularly when the treated sequences exceed 50-150 kb, depending on the algorithm. These problems have led us to design a probabilistic algorithm designated PAGEC which exponentially decreases the computing time (Courtois and Moncany 1995). This has been verified by testing comparisons of up to 4 Mb/4 Mb, which were achieved in 13 rain.…”

Section: Introductionmentioning

confidence: 94%

“…This has been verified by testing comparisons of up to 4 Mb/4 Mb, which were achieved in 13 rain. Furthermore, PAGEC is fast enough to permit an interactive use as it compares genomes as large as 325 kb in 20 s with a single index (Courtois and Moncany 1995). In this paper, PAGEC was applied to the immunodeficiency viruses.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Fast analysis of genomic homologies: Primate immunodeficiency virus

Moncany

Courtois

1996

J Mol Evol

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We have recently published a new probabilistic algorithm which performs genomic comparisons on a huge scale. In the present paper it was applied to immunodeficiency viral sequences extracted from international gene databanks. During global sequence analysis of human (HIV1 and HIV2) and simian viruses by means of dot-matrix representation, series of homology were obtained which permitted the definition of families of viruses overlapping the species divisions. Sequences of interest were characterized to the lexical base sentence through successive zoomings. Strain-to-strain comparison confirmed subfamily classifications and led, for example, to the identification of divergent LTR sequences. By way of example, we described the application of the algorithm to the ANT70C and MVP5180 HIV1-O viruses, for which the observed differences were shown to correspond to a deletion in the U3 region, situated between the LEF and NF-kappaB sites. It was of interest to consider these data in a tentative phylogenetic interpretation.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Fast analysis of genomic homologies: Primate immunodeficiency virus

Moncany

Courtois

1996

J Mol Evol

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Identification of conserved lentiviral sequences as landmarks of genomic flexibility

Moncany

Dalet

Courtois³

2006

Comptes Rendus. Biologies

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Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of 'species self' besides that of 'lentiviral self'. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported.

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A probabilistic algorithm for interactive huge genome comparison

Cited by 2 publications

References 0 publications

Fast analysis of genomic homologies: Primate immunodeficiency virus

Fast analysis of genomic homologies: Primate immunodeficiency virus

Identification of conserved lentiviral sequences as landmarks of genomic flexibility

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