Table 1

Dynamic Programming Connections in Prodigal

Left Node

Right Node

Connection Type

Connection Score


5' forward

3' forward

Gene

Start+coding score


3' reverse

5' reverse

Gene

Start+coding score


3' forward

5' forward

Intergenic Space

Distance modifiers


3' forward

3' reverse

Intergenic Space

Distance modifiers


5' reverse

3' reverse

Intergenic Space

Distance modifiers


5' reverse

5' forward

Intergenic Space

Distance modifiers


3' forward

3' forward

Overlapping Genes

Score of 2nd gene


3' reverse

3' reverse

Overlapping Genes

Score of 2nd gene


3' forward

5' reverse

Opposite Strand Overlap

Score of 2nd gene


Table 1 shows the types of dynamic programming connections in the algorithm. Each end of a gene is a node, and connections between these nodes represent either genes or the space between genes. The more complicated connections indicate overlapping genes.

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

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