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Figure 3 | BMC Bioinformatics

Figure 3

From: Motif-All: discovering all phosphorylation motifs

Figure 3

Performance comparison using data generated from PhosPhAt database 3.0. In Motif-All, we fix the p-value threshold to be 10-6 and report the results at the support threshold of 8% and 10%, respectively. Since it is not allowed to upload more than 10MB data to the Motif-X server, we set the “background” option of Motif-X to “IPI Arabidopsis Proteome” to mimic the background data in our local machine. As shown in [2], Motif-X is robust to the choice of background data. Therefore, it is acceptable to use such setting in the performance comparison. Since the occurrence threshold of Motif-X has a similar effect as the support constraint of Motif-All, we set this parameter to be the value that is equivalent to the support value of 8%, i.e., it is specified as 219, 33 and 6 for PhAtS, PhAtT and PhAtY, respectively. We download the Matlab codes of MoDL to perform motif discovery using its default configurations. The notation “[]” denotes a conserved position that match any letter contained in the bracket.

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