Learn to use MDscan, (Motif Discovery scan) a web-based submission to an algorithm for finding motifs on DNA sequences. This tool has particular applications to chromatin immunoprecipitation microarray experiments, better known as ChIP-chip experiments, and also to promoter discovery. MDscan finds DNA motifs which are shared among a set of sequences that you provide. You can submit your sequences to MDscan in FASTA format, specify a small number of required parameters, and the detailed results are emailed to you. In addition, MDscan provides a link to WebLogo, where you can obtain diagrammatic representations of motifs found in your sequences of interest. If you are involved in promoter discovery or perform ChIP-chip experiments, learn to use this tool for your data analysis needs.

You will learn:

  • how to create the appropriate input files
  • how to submit the data for analysis
  • how to access the results and interpret the output
  • how to obtain a WebLogo graphical representation of your data
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Motif analysis tools. You might find the other tutorials in the group interesting:

Melina II: A Web-Based Tool for Promoter Analysis

Gibbs Motif Sampler: A motif finder and analysis tool

Consensus: A pattern and motif recognition program

MEME Suite GLAM2 Algorithm: Part of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences.

MEME Algorithm: Multiple Expectation Maximum for Motif Elicitation

MEME Suite Overview: Motif-based sequence analysis tools

World Tour of Genomics Resources 2: Great tools from around the world

MEME Suite TOMTOM and GOMO algorithms: Motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provide


This tutorial is a part of the tutorial group Motifs and Domains. You might find the other tutorials in the group interesting:

Melina II: A Web-Based Tool for Promoter Analysis

MINT: Molecular Interaction Database

Gibbs Motif Sampler: A motif finder and analysis tool

MEME Suite Sequence Annotation Tools: MEME suite motif finding and annotating tools

PROSITE: Database of protein domains, families and functional sites

MEME Suite GLAM2 Algorithm: Part of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences.

MEME Algorithm: Multiple Expectation Maximum for Motif Elicitation

MEME Suite Overview: Motif-based sequence analysis tools

MEME Suite TOMTOM and GOMO algorithms: Motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provide

SMART: Protein domain annotation and analysis of domain architectures

InterPro: A comprehensive protein signature resource

CATEGORIES

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.

Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.

BLOG POSTS

What's the Answer? (promoter identification): BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to...

New On-line Tutorials on Promoter Analysis Tools: Comprehensive tutorials on a set of promoter analysis tools (Melina II, Consensus, MDscan, Gibbs and MEME) enable researchers to quickly and effectively use these invaluable resources. OpenHelix today ...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Liu Bingqiang et al., An integrative and applicable phylogenetic footprinting framework for cis -regulatory motifs identification in prokaryotic genomes Prokaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2982-x

Ruffing M. Anne et al., Genetic tools for advancement of Synechococcus sp. PCC 7002 as a cyanobacterial chassis. Microbial Cell Factories (2016) doi:10.1186/s12934-016-0584-6

Soares Miranda Michelle Prioli et al., Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera Multicellular invertebrate genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-576

Xiong Qian et al., Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors Human and rodent genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-587

Klepper Kjetil et al., MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis Sequence analysis (applications). BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-9