Assessing computational tools for the discovery of transcription factor binding sites
نویسندگان
چکیده
منابع مشابه
Comparative Analysis of Regulatory Motif Discovery Tools for Transcription Factor Binding Sites
In the post-genomic era, identification of specific regulatory motifs or transcription factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory networks, has emerged as an obstacle that frustrates many researchers. Consequently, numerous motif discovery tools and correlated databases have been applied to solving this problem. However, ...
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Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it remained unclear whether or not composite TFBS elements, commonly found in higher organisms where two or more TFBSs form functional complexes, could also be identified by using this approach. Here, we pre...
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MOTIVATION A variety of algorithms have been developed to predict transcription factor binding sites (TFBSs) within the genome by exploiting the evolutionary information implicit in multiple alignments of the genomes of related species. One such approach uses an extension of the standard position-specific motif model that incorporates phylogenetic information via a phylogenetic tree and a model...
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The discovery of gene regulatory elements requires the synergism between computational and experimental techniques in order to reveal the underlying regulatory mechanisms that drive gene expression in response to external cues and signals. Utilizing the large amount of high-throughput experimental data, constantly growing in recent years, researchers have attempted to decipher the patterns whic...
متن کاملDiscovery of novel transcription factor binding sites by statistical overrepresentation.
Understanding the complex and varied mechanisms that regulate gene expression is an important and challenging problem. A fundamental sub-problem is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be co-regulated. We discuss a computational method that identifies good candidates for such binding sites. Unlike local search techniques such as e...
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ژورنال
عنوان ژورنال: Nature Biotechnology
سال: 2005
ISSN: 1087-0156,1546-1696
DOI: 10.1038/nbt1053