Description
This track shows regions detected as putative genomic duplications within the
golden path. The following display conventions are used to distinguish
levels of similarity:
-
Light to dark gray: 90 - 98% similarity
-
Light to dark yellow: 98 - 99% similarity
-
Light to dark orange: greater than 99% similarity
-
Red: duplications of greater than 98% similarity that lack sufficient
Segmental Duplication Database evidence (most likely missed overlaps)
For a region to be included in the track, at least 1 Kb of the total
sequence (containing at least 500 bp of non-RepeatMasked sequence) had to
align and a sequence identity of at least 90% was required.
Methods
Segmental duplications play an important role in both genomic disease
and gene evolution. This track displays an analysis of the global
organization of these long-range segments of identity in genomic sequence.
Large recent duplications (>= 1 kb and >= 90% identity) were detected
by identifying high-copy repeats, removing these repeats from the genomic
sequence ("fuguization") and searching all sequence for similarity. The
repeats were then reinserted into the pairwise alignments, the ends of
alignments trimmed, and global alignments were generated.
For a full description of the "fuguization" detection method, see Bailey
et al., 2001. This method has become
known as WGAC (whole-genome assembly comparison); for example, see Bailey
et al., 2002.
Credits
These data were provided by Ginger Cheng, Xinwei She,
Archana Raja,
Tin Louie and
Evan Eichler
at the University of Washington.
References
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD,
Myers EW, Li PW, Eichler EE.
Recent segmental duplications in the human genome.
Science. 2002 Aug 9;297(5583):1003-7.
PMID: 12169732
Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE.
Segmental duplications: organization and impact within the
current human genome project assembly.
Genome Res. 2001 Jun;11(6):1005-17.
PMID: 11381028; PMC: PMC311093
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