Transcription factor binding site recognition by regularity matrices based on the natural classification method
نویسندگان
چکیده
A principally new approach to the classifications of nucleotide sequences based on the “natural” classification concept is proposed. As a result of “natural” classification of the nucleotide sequences, we obtain regularity matrices, where nucleotides are interconnected by regularities. Method, algorithm and software system DNANatClass for performing the “natural” classification have been developed. Experimental results comparing weight matrices with regularity matrices are presented. In this experiment, site recognition by regularity matrices appears to be more accurate than by weight matrixes.
منابع مشابه
SiTaR: a novel tool for transcription factor binding site prediction
MOTIVATION Prediction of transcription factor binding sites (TFBSs) is crucial for promoter modeling and network inference. Quality of the predictions is spoiled by numerous false positives, which persist as the main problem for all presently available TFBS search methods. RESULTS We suggest a novel approach, which is alternative to widely used position weight matrices (PWMs) and Hidden Marko...
متن کاملSimilarity Analysis between Transcription Factor Binding Sites by Bayesian Hypothesis Test
Transcription factor binding sites (TFBS) in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices (PFM). The ability to compare PFMs representing binding sites is especially important for de novo sequence motif discovery, where it is desirable to compare putative matrices to one another and to known matrices. We propose to identify and group similar pro...
متن کاملUse of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli
Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcription factor binding and that cannot be captured by the nucleotide sequence alon...
متن کاملRecognition of multiple patterns in unaligned sets of sequences. Comparison of kernel clustering method with other methods
MOTIVATION Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. RESULTS We developed a novel method for analysis o...
متن کاملA biophysical approach to transcription factor binding site discovery.
Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes. Here, we describe a novel bioinformatics method that bases classification of potential binding sites explicitly on the estimate of sequence-specific binding energy of a given transcription factor. Th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Intell. Data Anal.
دوره 12 شماره
صفحات -
تاریخ انتشار 2008