TAILIEUCHUNG - Báo cáo sinh học: " Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. | Kahn et al. Algorithms for Molecular Biology 2010 5 11 http content 5 1 11 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes Crystal L Kahn1 Shay Mozes1 Benjamin J Raphael1 2 Abstract Background Segmental duplications or low-copy repeats are common in mammalian genomes. In the human genome most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences. Results We describe a polynomial-time exact algorithm to compute duplication distance a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string. This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions. Finally we provide a description of a sequence of duplication events as a context-free grammar CFG . Conclusion These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes. Introduction Genomes evolve via many types of mutations ranging in scale from single nucleotide mutations to large genome rearrangements. Computational models of these mutational processes allow researchers to derive similarity measures between genome sequences and to reconstruct evolutionary relationships between genomes. For example considering chromosomal inversions as the only type of mutation leads to the so-called reversal distance problem of finding the minimum number of inversions reversals that transform one genome into another 1 . Several elegant polynomial-time algorithms have been found to solve this problem .

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