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...
| Main Authors: | , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Oxford University Press
2017
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| Online Access: | http://hdl.handle.net/1721.1/110128 https://orcid.org/0000-0003-0369-5269 https://orcid.org/0000-0002-3872-2856 |
| _version_ | 1826195321695240192 |
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| author | Wu, Xuebing Bartel, David |
| author2 | Massachusetts Institute of Technology. Computational and Systems Biology Program |
| author_facet | Massachusetts Institute of Technology. Computational and Systems Biology Program Wu, Xuebing Bartel, David |
| author_sort | Wu, Xuebing |
| collection | MIT |
| description | 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/. |
| first_indexed | 2024-09-23T10:11:01Z |
| format | Article |
| id | mit-1721.1/110128 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:11:01Z |
| publishDate | 2017 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/1101282022-09-30T19:27:46Z kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences Wu, Xuebing Bartel, David Massachusetts Institute of Technology. Computational and Systems Biology Program Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Biology Wu, Xuebing Bartel, David 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/. National Cancer Institute (U.S.) (GM118135) Helen Hay Whitney Foundation (Fellow) 2017-06-21T16:36:22Z 2017-06-21T16:36:22Z 2017-04 2017-04 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/110128 Wu, Xuebing, and David P. Bartel. “kpLogo: Positional k-Mer Analysis Reveals Hidden Specificity in Biological Sequences.” Nucleic Acids Research (April 29, 2017). https://orcid.org/0000-0003-0369-5269 https://orcid.org/0000-0002-3872-2856 en_US http://dx.doi.org/10.1093/nar/gkx323 Nucleic Acids Research Creative Commons Attribution-NonCommercial 4.0 International http://creativecommons.org/licenses/by-nc/4.0/ application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Wu, Xuebing Bartel, David kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences |
| title | kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences |
| title_full | kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences |
| title_fullStr | kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences |
| title_full_unstemmed | kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences |
| title_short | kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences |
| title_sort | kplogo positional k mer analysis reveals hidden specificity in biological sequences |
| url | http://hdl.handle.net/1721.1/110128 https://orcid.org/0000-0003-0369-5269 https://orcid.org/0000-0002-3872-2856 |
| work_keys_str_mv | AT wuxuebing kplogopositionalkmeranalysisrevealshiddenspecificityinbiologicalsequences AT barteldavid kplogopositionalkmeranalysisrevealshiddenspecificityinbiologicalsequences |