Short read DNA fragment anchoring algorithm

BMC Bioinformatics

Table 1 Coding results for variable sampling window length.

Sample window length	1	2	3	4	5	6	7	8	9
Vector count	4	10	20	35	56	84	120	165	220
Binary coding length	2	4	6	8	10	12	14	16	18
Vector coding length	2	4	5	6	6	7	7	8	8
Compression rate	0%	0%	16.7%	25%	40%	41.7%	50%	50%	55.6%

The compression rate is calculated as the difference between binary coding length and vector coding length divided by binary coding length. The vector count is calculated as C(w+m-1, w) where w is the sampling window length, m is the size of alphabet used to form the sequences. The vector coding length is the minimum value n which let 2ⁿ > vector count holds.

ISSN: 1471-2105