MICA: desktop software for comprehensive searching of DNA databases

BMC Bioinformatics

Table 2 Representative sizes, creation times, and loading times for MICA indexes

	K	Index Size (GB)	Index Creation Time (sec)	Index Loading Time (sec)
Chromosome 1 (2.46 × 10⁸ bases)	4	0.42	19.3	0.023
	6	0.44	27.1	0.024
Random Sequence (2.46 × 10⁸ bases)	4	0.46	23.5	0.020
	6	0.49	32.0	0.025
Human Genome (3.08 × 10⁹ bases)	4	5.33	262	0.49
	6	5.67	345	0.44

The sequences of chromosome 1 and the 25 chromosomes comprising the human genome were obtained from the Ensembl database. We also tested a computer-generated random sequence of 246,000,000 bp containing equal proportions of G, A, T, and C. Index size refers to index elements E – M of the MICA file (see Table 1), and does not include the Sequence Segment. The creation time for each index includes the time needed to write the index to disk, but does not include the additional time needed to embed a copy of the sequence within the file; this additional embedding time for chromosome 1 was 16.4 sec for K = 4 or 19.6 sec for K = 6. Index loading refers to the reading of elements A – C and E – J of an index from disk into memory. For the human genome, the values listed are the sums of the values for the individual chromosomes.

ISSN: 1471-2105