kpLogo: positionalk-mer analysis reveals hidden specificity in biological sequences

Motifs of only 1–4 letters can play important roles when present at key locations within macromolecules. Because existing motif-discovery tools typically miss these position-specific short motifs, we developed k pLogo, a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs. k pLogo also overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing ranked or weighted sequences increasingly available from high-throughput assays.