kpLogo: k-mer probability logo

k-mer probability logo (kpLogo) is a motif tool for integrated detection and visualization of positionally enriched or depleted k-mers from one or two sets of sequences of identical length.

Given a set of sequences, either weighted or unweighted, kpLogo performs statistical tests to find the most enriched and depleted short motif (k-mer) at each position, and visualizes the results using a new type of logo called k-mer logo, in which the most enriched/depleted k-mer at each position is plotted vertically and scaled by its statistical significance. In addition, kpLogo also outputs traditional logo plots for letter frequency, information content, and probability logo.

Cite:

Xuebing Wu and David Bartel (2017) kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences, see preprint in bioRxiv.




Copyright (c) 2017 Xuebing Wu