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FIGURE 9.4
Schematics for the sliding window algorithms for CGI extraction from human genome
sequences from [
8
]. (A) Set a 200-base window in the beginning of a contig (sequence),
compute
C
ECpG
ratio. Shift the window 1 bp after evaluation until
the window meets the criteria of a CGI. (B) If the window meets the criteria, shift the
window 200 bp and then evaluate again. (C and D) Repeat these 200 bp shifts until the
window does not meet the criteria. (E) Shift the last window 1 bp toward the 5
end until
it meets the criteria. (G) Evaluate
C
+
G
content and
O
/
ECpG
ratio. (H) If this large CGI
does not meet the criteria, trim 1 bp from each side until it meets the criteria. (I) Two
individual CGIs were connected if they were separated by less than 100 bp. (J) Values for
O
+
G
content and
O
/
G
content were recalculated to remain within the criteria. Reprinted
with permission from Takai, D., Jones, P. Comprehensive analysis of CpG islands in human
chromosomes 21 and 22.
PNAS
2002 99 (6) 3740-3745. Copyright (2002) National
Academy of Sciences, USA.
/
ECpG
and
C
+
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