ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

Table 1 Possible DNA sequences required to be looked-up in the brute force approach

Possible codons at each Position
1	2	3	4	5
I	R	G	R	E
ATT	CGT	GGT	CGT	GAA
ATC	CGC	GGC	CGC	GAG
ATA	CGA	GGA	CGA
	CGG	GGG	CGG
	AGA		AGA
	AGG		AGG

There are total 864 (3 × 6 × 4 × 6 × 2 = 864) possible DNA sequences created by combining codons from each position. Any combination, for example ATTCGTGGTCGTGAA, or the original sequence, ATCCGTGGGCGTGAG, can be translated to the same amino acid sequence IRGRE. The brute force approach is not practical because of the exponential growth in the number of possible sequences.

ISSN: 1471-2105

Possible codons at each Position
1	2	3	4	5
I	R	G	R	E
ATT	CGT	GGT	CGT	GAA
ATC	CGC	GGC	CGC	GAG
ATA	CGA	GGA	CGA
	CGG	GGG	CGG
	AGA		AGA
	AGG		AGG

Possible codons at each Position
1	2	3	4	5
I	R	G	R	E
ATT	CGT	GGT	CGT	GAA
ATC	CGC	GGC	CGC	GAG
ATA	CGA	GGA	CGA
	CGG	GGG	CGG
	AGA		AGA
	AGG		AGG

Possible codons at each Position
1	2	3	4	5
I	R	G	R	E
ATT	CGT	GGT	CGT	GAA
ATC	CGC	GGC	CGC	GAG
ATA	CGA	GGA	CGA
	CGG	GGG	CGG
	AGA		AGA
	AGG		AGG