yurasong/bioc2020workshop

Motif analysis with motifStack and dagLogo

github page | source code

Instructors and contact information

• Jianhong Ou: [email protected]
• Haibo Liu: [email protected]
• Lihua Julie Zhu: [email protected]

Workshop Description

A sequence motif is a short recurring pattern with biological significance such as a DNA recognition sequence for a transcription factor (TF), a mRNA splicing signal, or a functional region of a protein domain. To facilitate the analysis of binding site diversity/conservation within families of TFs and the evolution of binding sites between different species, we have developed a Bioconductor package motifStack. In this workshop, we will demonstrate the features and flexibility of motifStack for visualizing the alignment of multiple motifs in various styles. In addition, we will illustrate the utility of motifStack for providing insights into families of related motifs using a large collections of homeodomain (HD) DNA binding motifs from fly.

To take this workshop, participants are expected to have basic knowledge as follows: basic knowledge of R syntax, and basic knowledge of sequence motifs.

Ref: http://dx.doi.org/10.1038/nmeth.4555

Pre-requisites

• Basic knowledge of sequnce motifs
• Basic knowledge of R
• A computer with internet connection

Workshop Participation

• An overview of visualization of sequence motifs.
• Hands-on workshop learning how to do plot sequence logos with motifStack and dagLogo

R / Bioconductor packages used

• [motifStack]
• [dagLogo]
• [Biostrings]
• [MotifDb]
• [ggplot2]
• [colorBlindness]

Time outline

Activity	Time
Introduction of motifStack	10min
Sample code explanation	5min
Hands-on workshop	10min
Q & A	5 min

Workshop goals and objectives

Learning goals

1. Gain the knowledge of typical workflows for the generation, representation, alignment and visualization of DNA/RNA/amino acid motifs.

2. Learn how to visualize the alignment of multiple motifs in various styles using motifStack.

3. Become aware that experimental approaches, motif generation and alignment algorithms may affect motif alignment results and visualization.

Learning objectives

1. Learn how to import motifs from databases or a matrix.

2. Learn how to plot a single motif for DNA/RNA/AA.

3. Learn how to plot multiple motifs in various styles such as a linear tree and a radial tree.

4. Understand how to merge similar motifs and display the merged motif as motif signature.

5. Understand how to use various color options to highlight different motif features.