Figure 2.

Illustration of the dynamic programming connections in Prodigal. The red arrows represent gene connections, and the black arrows represent intergenic connections. (a) 5' forward to 3' forward: Gene on the forward strand. (b) 3' forward to 5' forward: Intergenic space between two forward strand genes. (c) 3' forward to 3' forward: Overlapping genes on the forward strand. (d) 3' forward to 5' reverse: Forward and reverse strand genes whose 3' ends overlap. (e) 5' reverse to 3' reverse: Intergenic space between two reverse strand genes. (f) 3' reverse to 5' reverse: Gene on the reverse strand. (g) 3' reverse to 3' reverse: Overlapping genes on the reverse strand. (h) 5' reverse to 5' forward: Intergenic space between two opposite strand genes. (i) 3' forward to 3' reverse: Intergenic space between two opposite strand genes.

Hyatt et al. BMC Bioinformatics 2010 11:119   doi:10.1186/1471-2105-11-119
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