Using Weeder for the discovery of conserved transcription factor binding sites

Current Protocols in Bioinformatics
Giulio Pavesi, Graziano Pesole

Abstract

One of the greatest challenges facing modern molecular biology is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors with their corresponding binding sites. Weeder is a software package freely available for non commercial users as a stand-alone or Web-based application for the automatic discovery of conserved motifs in a set of related DNA sequences from coregulated genes. The motifs found are likely to represent instances of binding sites for some common transcription factor regulating the genes of the set. The program has been designed to make its usage as simple as possible and to require very little prior knowledge about the length and conservation of the motifs to be found.

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
May 17, 2000·Bioinformatics·G D Stormo
Jun 12, 2002·Molecular Biology of the Cell·Michael L WhitfieldDavid Botstein
Dec 20, 2002·Nucleic Acids Research·Saurabh Sinha, Martin Tompa
Jun 26, 2003·Nucleic Acids Research·William ThompsonCharles E Lawrence
Jun 26, 2003·Nucleic Acids Research·Jacques van Helden
Oct 14, 2003·Bioinformatics·Chandrasegaran NarasimhanEdward Uberbacher
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Sep 24, 2004·Briefings in Bioinformatics·Giulio PavesiGraziano Pesole
May 4, 2005·Genome Research·W J KentDavid Haussler

❮ Previous
Next ❯

Citations

Jun 14, 2012·Nucleic Acids Research·Sebastian LuehrJohannes Söding
Feb 1, 2013·TheScientificWorldJournal·Hailin Chen, Vincent VanBuren
Aug 20, 2011·Genes & Development·Nellie MoshkovichElissa P Lei
Oct 18, 2011·BMC Genomics·M Aleksi KallioEija I Korpelainen
Feb 27, 2015·Archives of Toxicology·Onat KadiogluThomas Efferth
Dec 17, 2014·Genome Biology and Evolution·Alana V Beadell, Eric S Haag
Dec 19, 2012·Plant Molecular Biology·Leandro QuadranaMagdalena Rossi
Sep 20, 2012·Genome Research·Holger HartmannJohannes Söding

❮ 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.