Transcription factor motif quality assessment requires systematic comparative analysis
نویسندگان
چکیده
منابع مشابه
Transcription factor motif quality assessment requires systematic comparative analysis
Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions o...
متن کاملTranscription factor motif quality assessment requires
Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions o...
متن کاملComparative 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, ...
متن کاملDiscovering Transcription Factor Binding Motif Sequences
Introduction In biology, sequence motifs are short sequence patterns, usually with fixed lengths, that represent many features of DNA, RNA, and protein molecules. Sequence motifs can represent transcription factor binding sites for DNA, splice junctions for RNA, and binding domains for proteins. Thus, discovering sequence motifs can lead to a better understanding of transcriptional regulation, ...
متن کاملTheoretical and empirical quality assessment of transcription factor-binding motifs
Position-specific scoring matrices (PSSMs) are routinely used to predict transcription factor (TF)-binding sites in genome sequences. However, their reliability to predict novel binding sites can be far from optimum, due to the use of a small number of training sites or the inappropriate choice of parameters when building the matrix or when scanning sequences with it. Measures of matrix quality...
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ژورنال
عنوان ژورنال: F1000Research
سال: 2016
ISSN: 2046-1402
DOI: 10.12688/f1000research.7408.2