Caractérisation et analyse évolutive des répétitions intragéniques : une étude au niveau des gènes, des séquences protéiques et des structures tridimensionnelles

Abstract : Duplications play a major role in protein evolution and result in intragenic repeats found in about 14% of protein sequences. We chose to study these repeats from an evolutionary point of view. For this, we developed a program, Swelfe, that looks for repeats in genes, amino acid sequences and three dimensional structures of proteins. This program uses the same dynamic programming algorithm at all levels and a sequential representation of 3D structures. Repeat scores and significance tests are adapted at each level. We created a bank containing DNA sequences and amino acid sequences corresponding to PDB structures, and Swelfe was compared to DALI to validate our method concerning structural repeats. Finally this program is available at http://bioserv.rpbs.jussieu.fr/swelfe. Swelfe found an important number of repeats in a non redundant data set of DNA sequences, amino acid sequences and 3D structures and about 10% of proteins contain repeats at last at one level. However the repeat overlap at the three level is weak and most repeats are only found at one level, this confirm the relevance of studying repeats at three levels at the same time. The study of long structural repeats shows that about 30% of these repeats are symmetrical at 180°, as are the two elements of a homodimer. The analysis of these proteins shows that some of them could effectively replace homodimers.
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Life Sciences [q-bio]. Université Pierre et Marie Curie - Paris VI, 2008. French


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Contributor : Anne-Laure Abraham <>
Submitted on : Monday, May 10, 2010 - 12:17:36 PM
Last modification on : Wednesday, October 29, 2014 - 1:22:32 PM

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Anne-Laure Abraham. Caractérisation et analyse évolutive des répétitions intragéniques : une étude au niveau des gènes, des séquences protéiques et des structures tridimensionnelles. Life Sciences [q-bio]. Université Pierre et Marie Curie - Paris VI, 2008. French. <tel-00482373>

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