Related Experiment Video
Updated: Mar 3, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
PISMA: A Visual Representation of Motif Distribution in DNA Sequences
Rogelio Alcántara-Silva1, Moisés Alvarado-Hermida1, Gibrán Díaz-Contreras1
1División de Ingeniería Eléctrica, Facultad de Ingeniería, Universidad Nacional Autónoma de México (UNAM), México City, México.
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.
Related Concept Videos
DNA as a Genetic Template
DNA as a Genetic Template
DNA Microarrays
DNA Agarose Gel Electrophoresis
Gel extraction follows five major steps: running gel electrophoresis to separate fragments, isolating the individual bands, extracting DNA from those bands, and removing the dye and salts from the extracted mixture to obtain pure DNA.
In cloning experiments, both the insert and vector DNA...
The DNA Helix
The DNA Helix

