Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

Table 9 Compression and decompresson speed

	Average compression speed		Average decompression speed
	SP-86-ATOM	AA-15-DNA	SP-86-ATOM	AA-15-DNA
Gzip	0.14	0.40	0.03	0.06
Bzip2	0.26	0.51	0.09	0.16
PPMd16	0.57	0.67	0.61	0.80
PPMd8	0.46	0.65	0.50	0.76
PPMd4	0.34	0.47	0.36	0.53
PPMd2	0.31	0.51	0.33	0.53
Huffman	0.11	0.14	0.29	0.30
Ac fast	0.27	0.22	0.44	0.33
Rc fast	0.17	0.16	0.35	0.35
Ac med.	0.26	0.21	0.44	0.44
Rc med.	0.16	0.19	0.35	0.35
Ac slow	0.26	0.21	0.44	0.43
Rc slow	0.16	0.16	0.35	0.36
BwtRleHuff	0.23	0.43	0.27	0.31
BwtMtfRleHuff	0.23	0.36	0.28	0.32
BwtRleAc fast	0.28	0.38	0.35	0.46
BwtMtfRleAc fast	0.29	0.43	0.35	0.39
BwtRleRc fast	0.23	0.35	0.30	0.36
BwtMtfRleRc fast	0.24	0.37	0.31	0.35
BwtRleRc med.	0.23	0.36	0.30	0.31
BwtMtfRleRc med.	0.24	0.40	0.30	0.35
BwtRleRc slow	0.24	0.42	0.30	0.30
BwtMtfRleRc slow	0.24	0.42	0.31	0.32
BwtWavelet	0.25	0.39	0.43	0.31
Gencompress	-	7.00	-	1.54

Average compression (left) and decompression (right) speed, in μ-seconds per input symbol, for the SP-86-ATOM and AA-15-DNA data sets.

ISSN: 1471-2105