Table 1 Key aspects of HexDiff and other algorithms. The table shows the knowledge used and the parameters required by the different algorithms.
From: Using hexamers to predict cis-regulatory motifs in Drosophila
Algorithm | Knowledge Used | Parameters |
|---|---|---|
HexDiff | CRM Locations | Number of hexamers in Hd Window size Window score threshold |
Ahab | PWMs | Window size Free energy cutoff Order of background model |
Cluster Buster | PWMs | Motif score threshold Gap parameter Cluster score threshold Residue abundance range |
MSCAN | PWMs | Motif score threshold Window size Minimum hits Maximum hits |
MCAST | PWMs | Motif score threshold Maximum allowed distance between adjacent hits Pseudocount weight |
LWF | CRM Locations | String length Number of mismatches Detection window size Maximum number of channels Channels equalized Profile cutoff Peak width cutoff Smoothing window |