Check for PCR Recombinants

A simple tool that checks whether a sequence A is the recombination product of two sequence X and Y simply computes for each cross-over point k the minimum D*(k) of the Hamming distances of A to the two recombination products. Sequence positions for which D*(k) is minimal are likely crossover points. A sequence is a potential PCR recombinant if (i) it is within the Hamming distance DA of the allel test of a crossover product of two parents and (ii) if the distance to the recombinant is significantly smaller than the distance to closer one of the two parents. We define

f = [D*(min) - D(A,closer parent)]/( d(parent1,parent2)

as a measure of the decrease in Hamming distance. The table with the ``most likely'' recombinants show that none of the sequences is likely to be PCR recombinant.

 

Parameters: Thresholds: f_thr= 0.200 f_max = 15
genes sequence D f
###########*##*##*#####.##.##*#######################.#####.########.##.#####.### 7
HoxM_Z1 CACTTCAACCGCTACCTGACTCGTCGACGGCGCATCGAGATCGCCCACACCCTTTGCCTGAGTGAACGCCAAATCAAAATC
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_Z3 CACTTCAACCGTTATCTAACTCGTCGGCGACGCATCGAGATCGCCCACACCCTGTGCCTGAGTGAACGCCAGATCAAGATC
###########.##.##.#####.##*##.#######################*#####.########.##*#####*### 7
.................|||||||||...||||||||||||||||||||||||............................ 4 0.273
###########*##*##*#####.##.##*################.#.####.#####.########.##.#####.### 9
HoxM_X CACTTCAACCGCTACCTGACTCGTCGACGGCGCATCGAGATCGCCCGCGCCCTTTGCCTGAGTGAACGCCAAATCAAAATC
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_Z3 CACTTCAACCGTTATCTAACTCGTCGGCGACGCATCGAGATCGCCCACACCCTGTGCCTGAGTGAACGCCAGATCAAGATC
###########.##.##.#####.##*##.################*#*####*#####.########.##*#####*### 7
.................|||||||||...|||||||||||||||||................................... 4 0.231
########*##*##*#####.##.###*#.#####.#####*##.##..####.#####...###.##.############ 13
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_Z4 CACTTCAATCGGTATCTGACCCGACGGAGACGCATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
########.##.##.#####.##.###.#.#####*#####.##.##*.####.#####***###*##.############ 12
...........................||||||||......||||||.................................. 8 0.222
##.#####*##*##*#####.##*###*#*#####.#####*...##*.#.##.#####....##.##.############ 15
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
HoxM_Z4 CACTTCAATCGGTATCTGACCCGACGGAGACGCATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
##.#####.##.##.#####.##.###.#.#####*#####....##..#.##*#####***.##*##.############ 17
...............................................||||||............................ 10 0.217
########*##*##*#####.##.###*#.##*##.#####*##.##..####.#####...###.##.############ 13
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_U1 CACTTCAATCGGTATCTGACCCGTCGGAGACGGATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
########.##.##.#####.##.###.#.##.##*#####.##.##*.####.#####***###*##.############ 13
................................|||......||||||.................................. 8 0.263
##.#####*##*##*#####.##*###*#*##*##.#####*...##*.#.##.#####....##.##.############ 15
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
HoxM_U1 CACTTCAATCGGTATCTGACCCGTCGGAGACGGATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
##.#####.##.##.#####.##.###.#.##.##*#####....##..#.##*#####***.##*##.############ 18
...............................................||||||............................ 10 0.208
##*#####.##.##.#####.##.###.#.#*#########.##.###.####.##*###*#*###*#.############ 12
HoxM_Z4 CACTTCAATCGGTATCTGACCCGACGGAGACGCATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_W CATTTCAACCGCTACCTGACCCGGCGGCGGCCCATTGAGATCGCGCATGCCCTCTGTCTCACCGAGAGGCAGATCAAGATC
##.#####*##*##*#####.##.###*#.#.#########*##.###.####*##.###.#.###.#.############ 12
.....................................................|||......................... 8 0.222
##*#####.##.##.#####.##.###.#.#####.#####.***##.*#*##.#####...*##.##.############ 16
HoxM_Z4 CACTTCAATCGGTATCTGACCCGACGGAGACGCATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
##.#####*##*##*#####.##*###*#*#####.#####*...##*.#.##.#####....##.##.############ 15
.........................................|....................................... 10 0.217
##*#####.##.##.#####.##.###.#.###########.**.##*.#*##.########*#####.############ 12
HoxM_Z4 CACTTCAATCGGTATCTGACCCGACGGAGACGCATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
##.#####*##*##*#####.##.###*#.###########*...##..#.##.########.#####*############ 12
.........................................|....................................... 8 0.222
##*#####.##.##.#####.##.###.#.#*.########.##.###.####.##*###*#*###*#.############ 13
HoxM_U1 CACTTCAATCGGTATCTGACCCGTCGGAGACGGATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_W CATTTCAACCGCTACCTGACCCGGCGGCGGCCCATTGAGATCGCGCATGCCCTCTGTCTCACCGAGAGGCAGATCAAGATC
##.#####*##*##*#####.##.###*#.#.*########*##.###.####*##.###.#.###.#.############ 12
.....................................................|||......................... 8 0.211
##*#####.##.##.#####.##.###.#.##.##.#####.***##.*#*##.#####...*##.##.############ 17
HoxM_U1 CACTTCAATCGGTATCTGACCCGTCGGAGACGGATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
HoxM_Z2 CACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
##.#####*##*##*#####.##*###*#*##*##.#####*...##*.#.##.#####....##.##.############ 15
.........................................|....................................... 10 0.208
##*#####.##.##.#####.##.###.#.##.########.**.##*.#*##.########*#####.############ 13
HoxM_U1 CACTTCAATCGGTATCTGACCCGTCGGAGACGGATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
##.#####*##*##*#####.##.###*#.##*########*...##..#.##.########.#####*############ 12
.........................................|....................................... 8 0.211
##.#################.##.#####.#*##########...##..#.##.##*###*#.###*#*############ 12
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
HoxM_W CATTTCAACCGCTACCTGACCCGGCGGCGGCCCATTGAGATCGCGCATGCCCTCTGTCTCACCGAGAGGCAGATCAAGATC
##*#################.##*#####*#.##########..*##.*#.##.##.###.#.###.#.############ 12
................................................||||||||......................... 8 0.235
##.#################.##.#####.#.##########**.##*.#*##*##.###.#.###.#.############ 12
HoxM_W CATTTCAACCGCTACCTGACCCGGCGGCGGCCCATTGAGATCGCGCATGCCCTCTGTCTCACCGAGAGGCAGATCAAGATC
HoxM_Y CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC
HoxM_U2 CATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATC
##.#################.##.#####.#*##########...##..#.##.##*###*#.###*#*############ 12
.....................................................|||......................... 8 0.235