Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics

Table 7

Comparison of pipeline-based time-to-solutions with ideal limits. Ideal limits are obtained from the benchmark results of 20 sequences divided by the number of cores in an instance. Units are minutes.

Tools	Pipeline	Ideal limit	Pipeline	Ideal limit	Pipeline	Ideal limit
	m1.small		c1.xlarge		hi1.4xlarge
SAMT2K	1271.0	1055.7	224.5	65.6	168.3	35.7
SP3	1312.2	1124.4	118.6	68.1	105.7	33.0
CSBLAST	25.2	15.4	6.0	1.23	4.4	0.47
HMMER	29.0	16.0	6.1	1.0	5.8	0.6
pfTools	244.8	226.0	18.3	12.8	15.5	9.2
THREADER	27842.2	23744.0	2019.3	1488.0	1552.2	1090.4
SPARKS	1021.8	1037.7	80.0	54.3	73.3	41.8