Correction: Frequent Gain and Loss of Functional Transcription Factor Binding Sites
نویسندگان
چکیده
منابع مشابه
Frequent Gain and Loss of Functional Transcription Factor Binding Sites
Cis-regulatory sequences are not always conserved across species. Divergence within cis-regulatory sequences may result from the evolution of species-specific patterns of gene expression or the flexible nature of the cis-regulatory code. The identification of functional divergence in cis-regulatory sequences is therefore important for both understanding the role of gene regulation in evolution ...
متن کاملEvolution of transcription factor DNA binding sites.
In bioinformatics, binding of transcription regulatory factors to the cognate binding sites is usually described by sequence-specific binding energy, which is estimated from a training sample of sites. This model implies that all binding sites with binding energy above some threshold are functional and site sequence variations should be considered neutral until they do not reduce this energy be...
متن کاملPseudocounts for transcription factor binding sites
To represent the sequence specificity of transcription factors, the position weight matrix (PWM) is widely used. In most cases, each element is defined as a log likelihood ratio of a base appearing at a certain position, which is estimated from a finite number of known binding sites. To avoid bias due to this small sample size, a certain numeric value, called a pseudocount, is usually allocated...
متن کاملInformation Content in Transcription Factor Binding Sites
The application of Information Theory to the analysis of genomic sequences and, specifically, transcription factor binding sites, is one of the most successful attempts at modeling the behavior and evolution of these genomic elements. As such, information theory models lie at the core of many transcription factor binding site search and motif discovery tools, such as the widely used Virtual Foo...
متن کاملDiscovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.
Completing the annotation of a genome sequence requires identifying the regulatory sequences that control gene expression. To identify these sequences, we developed an algorithm that searches for short, conserved sequence motifs in the genomes of related species. The method is effective in finding motifs de novo and for refining known regulatory motifs in Saccharomyces cerevisiae. We tested one...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2009
ISSN: 1553-7358
DOI: 10.1371/annotation/363b6074-caec-4238-b88f-acbf45de498f