Logomaker: beautiful sequence logos in Python
Abstract Summary Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creati...
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| Published in | Bioinformatics Vol. 36; no. 7; pp. 2272 - 2274 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.04.2020
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Abstract
Summary
Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment. Logos are rendered as native matplotlib objects that are easy to stylize and incorporate into multi-panel figures.
Availability and implementation
Logomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Documentation is provided at http://logomaker.readthedocs.io; source code is available at http://github.com/jbkinney/logomaker. |
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| AbstractList | Abstract
Summary
Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment. Logos are rendered as native matplotlib objects that are easy to stylize and incorporate into multi-panel figures.
Availability and implementation
Logomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Documentation is provided at http://logomaker.readthedocs.io; source code is available at http://github.com/jbkinney/logomaker. Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment. Logos are rendered as native matplotlib objects that are easy to stylize and incorporate into multi-panel figures.SUMMARYSequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment. Logos are rendered as native matplotlib objects that are easy to stylize and incorporate into multi-panel figures.Logomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Documentation is provided at http://logomaker.readthedocs.io; source code is available at http://github.com/jbkinney/logomaker.AVAILABILITY AND IMPLEMENTATIONLogomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Documentation is provided at http://logomaker.readthedocs.io; source code is available at http://github.com/jbkinney/logomaker. Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment. Logos are rendered as native matplotlib objects that are easy to stylize and incorporate into multi-panel figures. Logomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Documentation is provided at http://logomaker.readthedocs.io; source code is available at http://github.com/jbkinney/logomaker. |
| Author | Kinney, Justin B Tareen, Ammar |
| AuthorAffiliation | Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory , Cold Spring Harbor, NY 11724, USA |
| AuthorAffiliation_xml | – name: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory , Cold Spring Harbor, NY 11724, USA |
| Author_xml | – sequence: 1 givenname: Ammar surname: Tareen fullname: Tareen, Ammar organization: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA – sequence: 2 givenname: Justin B surname: Kinney fullname: Kinney, Justin B email: jkinney@cshl.edu organization: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31821414$$D View this record in MEDLINE/PubMed |
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Summary
Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently... Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to... |
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| Title | Logomaker: beautiful sequence logos in Python |
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