Table 6

Coding region boundary classifiers. Coding region boundary classifiers. Window sizes and positions are shown for the five coding region boundary classifiers used by CONTRAST. Coordinates are defined such that the boundary occurs between the adjacent positions -1 and 1 (that is, either position -1 is coding and position 1 is coding or the reverse is true), with coordinates increasing in the 5' to 3' direction. Each classifier's require consensus sequence is shown in the second column.

Consensus

5' end

3' end

Length


Start codon

A1T2G3

-8

6

14

Stop codon

T1A2A3, T1A2G3, T1G2A3

1

6

6

Donor splice GT

G1T2

-3

8

11

Donor splice GC

G1C2

-3

8

11

Acceptor splice

A-2G-1

-27

3

30


Gross et al. Genome Biology 2007 8:R269   doi:10.1186/gb-2007-8-12-r269

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