Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation.

Nature Protocols
Yannick HaudryLaurence Ettwiller

Abstract

Genome-wide location analysis has become a standard technology to unravel gene regulation networks. The accurate characterization of nucleotide signatures in sequences is key to uncovering the regulatory logic but remains a computational challenge. This protocol describes how to best characterize these signatures (motifs) using the new standalone version of Trawler, which was designed and optimized to analyze chromatin immunoprecipitation (ChIP) data sets. In particular, we describe the three main steps of Trawler_standalone (motif discovery, clustering and visualization) and discuss the appropriate parameters to be used in each step depending on the data set and the biological questions addressed. Compared to five other motif discovery programs, Trawler_standalone is in most cases the fastest algorithm to accurately predict the correct motifs especially for large data sets. Its running time ranges within few seconds to several minutes, depending on the size of the data set and the parameters used. This protocol is best suited for bioinformaticians seeking to use Trawler_standalone in a high-throughput manner.

References

Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Jan 19, 2002·Genes & Development·Bing RenBrian David Dynlacht
Feb 13, 2004·Bioinformatics·Michele ClampGeoffrey J Barton
Apr 3, 2004·Genome Research·Mathieu BlanchetteWebb Miller
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Mar 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Xinmin ZhangMarc Montminy
Jun 28, 2005·Nucleic Acids Research·Stefan RoepckeMartin Vingron
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
Jan 24, 2007·Molecular and Cellular Biology·Peter S LinsleyLee Lim
Apr 28, 2007·Science·Antony RodriguezAllan Bradley
Jun 26, 2007·Nature Methods·Laurence EttwillerJoachim Wittbrodt
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Dec 19, 2007·Nucleic Acids Research·D KarolchikW J Kent

❮ Previous
Next ❯

Citations

Nov 10, 2010·BMC Bioinformatics·Fernando Garcia-AlcaldeAdrian J Shepherd
Mar 11, 2011·PloS One·Benjamin D WegerThomas Dickmeis
Apr 13, 2011·PloS One·Stuart K ArcherChristine Clayton
May 20, 2015·Naunyn-Schmiedeberg's Archives of Pharmacology·Simon R FosterMirana Ramialison
Aug 5, 2020·Cold Spring Harbor Protocols·James DeCaprio, Thomas O Kohl
Feb 10, 2012·Development·Mirana RamialisonJoachim Wittbrodt

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.