Prodigal: prokaryotic gene recognition and translation initiation site identification

BMC Bioinformatics

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 2^nd gene
3' reverse	3' reverse	Overlapping Genes	Score of 2^nd gene
3' forward	5' reverse	Opposite Strand Overlap	Score of 2^nd 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.

ISSN: 1471-2105