| This tool computationally predicts CTCF sites for a nucleotide sequence located on the forward strand. The user is required to provide two files as inputs. The first is the nucleotide sequence of interest on the + strand in FASTA format (this can be obtained from UCSC genome browser or Ensembl). The second file must be a FASTA formatted file containing the chromosome number and the genomic position of the first nucleotide sequence (separated by a tab). For example, if the sequence of interest is located on chromosome 3 with a starting genomic position of 1850000, the first line of the second input file must start with a fasta tag, and the second line will be chr3 1850000
Details of Algorithm: CTCF sites are predicted by applying the following equation w(X,j) = log2 (((f(X,j) + sqrt(N) x b(X)) / (N + sqrt(N))) / b(X)) Where w(X,j) is the weight of nucleotide X at position j, N is the total number of binding sites or the sum of all nucleotide occurrences in the column, and b is the prior background frequency of the nucleotide X. The sum of weights for corresponding nucleotides at each column of the matrix then estimates the likelihood of any sequence of length m to be an instance of a CTCF binding site and takes into account the GC content of the genomic region being scanned. Citation and further help: For further details of the algorithm, please refer to Khan MA, Soto-Jimenez LM, Howe T, Streit A, Sosinsky A, Stern CD (2013). Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome.. Genesis, , - . doi:10.1002/dvg.22375 |
hg clone https://toolshed.g2.bx.psu.edu/repos/mkhan1980/ctcf_analysis
| Name | Description | Version | Minimum Galaxy Version |
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| 1.0.0 | any | ||
| 1.0.0 | any | ||