<tool id="fa_gc_content_1" name="Discover CTCF Sites for Forward Strand">
      <description></description>
      <command interpreter="perl">check.pl $input $input2 $output</command>
      <inputs>
        <param format="fasta" name="input" type="data" label="Forward Strand Sequence File"/>
 <param format="fasta" name="input2" type="data" label="Forward Strand Coordinate file"/>
      </inputs>


      <outputs>
      <data format="tabular" name="output" />
    </outputs>
  
    <tests>
      <test>
        <param name="input" value="fa_gc_content_input.fa"/>
        <param name="input2" value="fa_gc_content_input2.fa"/>
 <output name="out_file1" file="concatenated.txt"/>
      </test>
    </tests>
  
    <help>
Background:
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(σ,j) = log2 (((f(σ,j) + sqrt(N) x b(σ)) / (N + sqrt(N))) / b(σ))

Where w(σ,j) is the weight of nucleotide σ 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 σ. 

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 
 
For queries/questions, email ucbtmaf@ucl.ac.uk    
    </help>

  
  </tool>