kpLogo: positional k-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 kpLogo, a probability-based logo tool for integrated detection and visualization of positi...

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Bibliographic Details
Published in:Nucleic acids research 2017-07, Vol.45 (W1), p.W534-W538
Main Authors: Wu, Xuebing, Bartel, David P
Format: Article
Language:English
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Summary: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 kpLogo, a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences. kpLogo 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. kpLogo can be found at http://kplogo.wi.mit.edu/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx323