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PISMA：DNA序列中基序分布的可视化表示。

PISMA: A Visual Representation of Motif Distribution in DNA Sequences.

作者信息

Alcántara-Silva Rogelio, Alvarado-Hermida Moisés, Díaz-Contreras Gibrán, Sánchez-Barrios Martha, Carrera Samantha, Galván Silvia Carolina

机构信息

División de Ingeniería Eléctrica, Facultad de Ingeniería, Universidad Nacional Autónoma de México (UNAM), México City, México.

Unidad de Posgrado, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México City, México.

出版信息

Bioinform Biol Insights. 2017 Mar 30;11:1177932217700907. doi: 10.1177/1177932217700907. eCollection 2017.

DOI:10.1177/1177932217700907
PMID:28469418
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5390925/
Abstract

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.

摘要

背景

由于基序分布的图形化展示和分析可为实验假设提供见解，PISMA旨在识别DNA序列上的基序，进行计数并以图形方式展示。基序长度范围为2至10个碱基，DNA序列长度可达10 kb。基序分布以类似条形码、类似基因图谱和转录本模式的形式展示。

结果

我们获得了来自91个人乳头瘤病毒基因组的CpG位点分布的图形化模式。此外，我们展示了两项分析：一项是与抗甲基化或甲基化敏感的CpG岛相关的DNA基序分析，另一项是与外泌体RNA分泌相关的基序分析。

可用性与实现方式

PISMA是用Java开发的；它可在任何类型的硬件和多种操作系统中执行。非商业用户可免费使用PISMA。英文版本和用户手册在补充文件1和2中提供，西班牙语版本可在www.biomedicas.unam.mx/wp-content/software/pisma.zip和www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/105e3be978ef/10.1177_1177932217700907-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/4dd0a2b3bb97/10.1177_1177932217700907-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/b61f8da378d1/10.1177_1177932217700907-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/67353faa72d0/10.1177_1177932217700907-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/fd2fe84f12bd/10.1177_1177932217700907-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/c736c6c3752d/10.1177_1177932217700907-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/105e3be978ef/10.1177_1177932217700907-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/4dd0a2b3bb97/10.1177_1177932217700907-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/b61f8da378d1/10.1177_1177932217700907-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/67353faa72d0/10.1177_1177932217700907-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/fd2fe84f12bd/10.1177_1177932217700907-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/c736c6c3752d/10.1177_1177932217700907-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2040/5390925/105e3be978ef/10.1177_1177932217700907-fig6.jpg

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