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

Table 8 Compression ratio

	CK-36-PDB	CK-36-REL	CK-36-SEQ	SP-86-ATOM	SP-86-PDB	AA-15-DNA
Gzip	6.434	13.173	21.271	2.133	6.214	2.415
Bzip2	6.696	16.104	26.808	1.503	6.522	2.197
PPMd16	6.846	13.303	22.996	1.463	6.641	2.108
PPMd8	6.846	13.303	22.996	1.422	6.641	2.109
PPMd4	6.846	13.316	23.043	1.565	6.641	2.047
PPMd2	6.828	13.310	22.996	2.045	6.627	1.966
Huffman	6.307	14.356	25.867	3.590	6.095	2.152
Ac fast	6.991	16.903	28.847	3.573	6.711	1.951
Rc fast	6.952	17.170	30.337	3.581	6.679	1.955
Ac med.	6.650	15.682	27.718	3.533	6.411	1.951
Rc med.	6.631	15.929	29.161	3.536	6.391	1.956
Ac slow	6.350	14.551	26.745	3.542	6.140	1.955
Rc slow	6.364	14.954	28.298	3.545	6.153	1.958
BwtRleHuff	6.580	15.402	28.298	1.849	6.355	2.271
BwtMtfRleHuff	6.589	15.064	27.796	1.644	6.313	2.138
BwtRleAc fast	7.300	18.002	31.592	1.557	6.989	2.141
BwtMtfRleAc fast	7.393	17.345	30.933	1.491	7.033	2.037
BwtRleRc fast	7.266	18.281	33.224	1.558	6.962	2.145
BwtMtfRleRc fast	7.360	17.534	32.376	1.493	7.007	2.041
BwtRleRc med.	6.932	16.981	31.922	1.677	6.667	2.142
BwtMtfRleRc med.	7.025	16.455	31.294	1.561	6.715	2.035
BwtRleRc slow	6.654	15.961	30.824	1.793	6.415	2.142
BwtMtfRleRc slow	6.755	15.669	30.478	1.614	6.473	2.034
BwtWavelet	6.913	15.019	27.686	1.607	6.734	2.188
Gencompress	-	-	-	-	-	1.933

Average compression ratio, in bits per symbol, of the tested algorithms for the six data sets.

ISSN: 1471-2105