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PISMA: A Visual Representation of Motif Distribution in DNA Sequences

BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to...

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Autores principales: Alcántara-Silva, Rogelio, Alvarado-Hermida, Moisés, Díaz-Contreras, Gibrán, Sánchez-Barrios, Martha, Carrera, Samantha, Galván, Silvia Carolina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: SAGE Publications 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390925/
https://www.ncbi.nlm.nih.gov/pubmed/28469418
http://dx.doi.org/10.1177/1177932217700907
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author Alcántara-Silva, Rogelio
Alvarado-Hermida, Moisés
Díaz-Contreras, Gibrán
Sánchez-Barrios, Martha
Carrera, Samantha
Galván, Silvia Carolina
author_facet Alcántara-Silva, Rogelio
Alvarado-Hermida, Moisés
Díaz-Contreras, Gibrán
Sánchez-Barrios, Martha
Carrera, Samantha
Galván, Silvia Carolina
author_sort Alcántara-Silva, Rogelio
collection PubMed
description BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. RESULTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. AVAILABILITY AND IMPLEMENTATION: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf.
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spelling pubmed-53909252017-05-03 PISMA: A Visual Representation of Motif Distribution in DNA Sequences Alcántara-Silva, Rogelio Alvarado-Hermida, Moisés Díaz-Contreras, Gibrán Sánchez-Barrios, Martha Carrera, Samantha Galván, Silvia Carolina Bioinform Biol Insights Methodology BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. RESULTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. AVAILABILITY AND IMPLEMENTATION: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf. SAGE Publications 2017-03-30 /pmc/articles/PMC5390925/ /pubmed/28469418 http://dx.doi.org/10.1177/1177932217700907 Text en © The Author(s) 2017 http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page(https://us.sagepub.com/en-us/nam/open-access-at-sage).
spellingShingle Methodology
Alcántara-Silva, Rogelio
Alvarado-Hermida, Moisés
Díaz-Contreras, Gibrán
Sánchez-Barrios, Martha
Carrera, Samantha
Galván, Silvia Carolina
PISMA: A Visual Representation of Motif Distribution in DNA Sequences
title PISMA: A Visual Representation of Motif Distribution in DNA Sequences
title_full PISMA: A Visual Representation of Motif Distribution in DNA Sequences
title_fullStr PISMA: A Visual Representation of Motif Distribution in DNA Sequences
title_full_unstemmed PISMA: A Visual Representation of Motif Distribution in DNA Sequences
title_short PISMA: A Visual Representation of Motif Distribution in DNA Sequences
title_sort pisma: a visual representation of motif distribution in dna sequences
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390925/
https://www.ncbi.nlm.nih.gov/pubmed/28469418
http://dx.doi.org/10.1177/1177932217700907
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