THE NEW APPROACH OF BOTH NEW AND OLD SEGMENTAL DUPLICATIONS SEARCH: REPETITIVE DNA AS A MOLECULAR ARCHAEOLOGY TOOL

Motivation: The mechanism of segmental duplications remains unclear. The main approach for duplicon hunting is the pairwise alignment of “unique” (masked from the known repetitive elements) DNAs. The preferred centromere-proximal location of segmental duplications in the human genome implies the possible participation of (peri)centric repeats in their distribution. The high frequency of genomic repeats at the duplicons termini let us think, that there could be much more repeat-linked duplications. Results:We used our own consensi for human satellite subfamilies for new human repetitive elements library (tested for use with the RepeatMasker program). Using modified Smith-Waterman method for detecting repetitive elements, we have produced the detailed repeats map in 34 build of the human genome. We have suggested and tested the new approach for detecting both recent and old duplicons, according to repeat maps pairwise comparison. Availability: The RepeatsCompare program, human repeats library and test data are available upon e-mail request: nixie@eimb.relarn.ru.