Learn to use theTOMTOM and GOMO algorithms, which are part of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provide. The results are emailed to you and are available on the web, and offer extensive computational and schematic details of the motifs it has found, with links to more information and additional analysis features. TOMTOM compares an input DNA motif to known motifs in a database and outputs a ranked list of matching motifs. GOMO analyzes a motif and returns a list of GO-terms that are significantly associated with genes containing the motif.

You will learn:

  • to submit a motif to TOMTOM
  • to understand the TOMTOM output display options and features
  • to submit a query to the GOMO tool
  • to understand output display options and features of the GOMO tool
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

MDscan: Motif Discovery scan for nucleotide and protein motifs

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


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

MDscan: Motif Discovery scan for nucleotide and protein motifs

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

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.

BLOG POSTS

Video Tip of the Week: Ambiscript Mosaic for visualizing nucleotide motifs: One of the topics I keep an eye on is visualization of various types of genomics data, and I'm always interested in new tools for graphical representations. In the past some of our most popular posts h...

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...

Tip of the Week: Melina II for promoter analysis: One of the most frequently-asked questions we get when we are out doing workshops is: how do I find motifs in promoters, and what can I do with them to find more information? Just last Friday we were ...

Tip of the Week: MEME Suite of Motif Discovery Tools: In this week's tip I'm going to introduce you to a suite of motif discovery tools, and show you (briefly) how to use one of the tools. The MEME suite is a comprehensive collection of tools for analysi...

BIOMED CENTRAL

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