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SlimShadey: A manipulation tool for multiple sequence alignments
The visualization of sequence alignments with the addition of meaningful shading and annotation is critical to convey the importance of structural elements, domains, motifs, and individual residues. Hence, we have developed a JavaFX based software package (SlimShadey) with an intuitive graphical use...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10599665/ https://www.ncbi.nlm.nih.gov/pubmed/37886161 http://dx.doi.org/10.6026/97320630019659 |
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author | Shah, Avi Aneesha, Kodati Sudhir, Nayak |
author_facet | Shah, Avi Aneesha, Kodati Sudhir, Nayak |
author_sort | Shah, Avi |
collection | PubMed |
description | The visualization of sequence alignments with the addition of meaningful shading and annotation is critical to convey the importance of structural elements, domains, motifs, and individual residues. Hence, we have developed a JavaFX based software package (SlimShadey) with an intuitive graphical user interface that allows for the creation and visualization of features on sequence alignments, as well as trimming and editing of subsequences. SlimShadey will run without modification on Windows 7 (or higher) and will also run on OS X / macOS, most Linux distributions, and servers. SlimShadey features real-time shading and comparison of residues based on user-defined measures of conservation such as frequency, user-selected substitution matrices, composition-based consensus sequence, regular expressions, and hidden Markov models. The software also allows users to generate custom sequence logos, configurable publication quality images of alignments with shading and annotation, and shareable self-contained project files for collaboration. SlimShadey is an open source freely available Java program. Compiled .jar executables, source code, supplementary materials including the user manual, links to video tutorials, and all sample data are available through the URLS at availability. |
format | Online Article Text |
id | pubmed-10599665 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
spelling | pubmed-105996652023-10-26 SlimShadey: A manipulation tool for multiple sequence alignments Shah, Avi Aneesha, Kodati Sudhir, Nayak Bioinformation Research Article The visualization of sequence alignments with the addition of meaningful shading and annotation is critical to convey the importance of structural elements, domains, motifs, and individual residues. Hence, we have developed a JavaFX based software package (SlimShadey) with an intuitive graphical user interface that allows for the creation and visualization of features on sequence alignments, as well as trimming and editing of subsequences. SlimShadey will run without modification on Windows 7 (or higher) and will also run on OS X / macOS, most Linux distributions, and servers. SlimShadey features real-time shading and comparison of residues based on user-defined measures of conservation such as frequency, user-selected substitution matrices, composition-based consensus sequence, regular expressions, and hidden Markov models. The software also allows users to generate custom sequence logos, configurable publication quality images of alignments with shading and annotation, and shareable self-contained project files for collaboration. SlimShadey is an open source freely available Java program. Compiled .jar executables, source code, supplementary materials including the user manual, links to video tutorials, and all sample data are available through the URLS at availability. Biomedical Informatics 2023-05-31 /pmc/articles/PMC10599665/ /pubmed/37886161 http://dx.doi.org/10.6026/97320630019659 Text en © 2023 Biomedical Informatics https://creativecommons.org/licenses/by/3.0/This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |
spellingShingle | Research Article Shah, Avi Aneesha, Kodati Sudhir, Nayak SlimShadey: A manipulation tool for multiple sequence alignments |
title | SlimShadey: A manipulation tool for multiple sequence alignments |
title_full | SlimShadey: A manipulation tool for multiple sequence alignments |
title_fullStr | SlimShadey: A manipulation tool for multiple sequence alignments |
title_full_unstemmed | SlimShadey: A manipulation tool for multiple sequence alignments |
title_short | SlimShadey: A manipulation tool for multiple sequence alignments |
title_sort | slimshadey: a manipulation tool for multiple sequence alignments |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10599665/ https://www.ncbi.nlm.nih.gov/pubmed/37886161 http://dx.doi.org/10.6026/97320630019659 |
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