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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.

From: STEM: a tool for the analysis of short time series gene expression data

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