Table 1

Comparison of time series microarray software packages. The table presents a comparison of three microarray time series analysis software packages: STEM, GQL, and CAGED. The execution time results are based on running on the same dataset as in Figure 3. The default settings of STEM and CAGED were used. For GQL the initial collection of HMMs was set to six two state HMMs and six three state HMMs. The experiments were carried out on a Pentium 1 GHz with 512 MB of RAM.

Software

Type of time series most appropriate for

Comparison Support

Cluster to GO Support

GO to Cluster Support

Automated Reports

Execution Time


STEM

short

Yes

Yes

Yes

No

17s

GQL

long

No

Yes

No

No

82s

CAGED

long

No

No

No

Yes

145s


Ernst and Bar-Joseph BMC Bioinformatics 2006 7:191   doi:10.1186/1471-2105-7-191

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