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2015 ; 11
(ä): 253-61
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Segmenting the Human Genome into Isochores
#MMPMID26640363
Cozzi P
; Milanesi L
; Bernardi G
Evol Bioinform Online
2015[]; 11
(ä): 253-61
PMID26640363
show ga
The human genome is a mosaic of isochores, which are long (>200 kb) DNA sequences
that are fairly homogeneous in base composition and can be assigned to five
families comprising 33%-59% of GC composition. Although the compartmentalized
organization of the mammalian genome has been investigated for more than 40
years, no satisfactory automatic procedure for segmenting the genome into
isochores is available so far. We present a critical discussion of the currently
available methods and a new approach called isoSegmenter which allows segmenting
the genome into isochores in a fast and completely automatic manner. This
approach relies on two types of experimentally defined parameters, the
compositional boundaries of isochore families and an optimal window size of 100
kb. The approach represents an improvement over the existing methods, is ideally
suited for investigating long-range features of sequenced and assembled genomes,
and is publicly available at https://github.com/bunop/isoSegmenter.