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KpLogo: positional k-mer analysis reveals hidden specificity in biological sequences.

ABSTRACT: 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/.

SUBMITTER: Wu X

PROVIDER: S-EPMC5570168 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences.

Wu Xuebing X Bartel David P DP

Nucleic acids research 20170701 W1

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 r ...[more]

PMID: 28460012

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