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1 <tool id="fa_gc_content_2" name="Discover CTCF Sites for Reverse Strand">
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2 <description></description>
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3 <command interpreter="perl">check2.pl $input $input2 $output</command>
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4 <inputs>
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5 <param format="fasta" name="input" type="data" label="Reverse Strand Sequence File"/>
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6 <param format="fasta" name="input2" type="data" label="Reverse Strand Coordinate file"/>
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7 </inputs>
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8
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9
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10 <outputs>
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11 <data format="tabular" name="output" />
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12 </outputs>
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13
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14 <tests>
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15 <test>
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16 <param name="input" value="fa_gc_content_input3.fa"/>
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17 <param name="input2" value="fa_gc_content_input4.fa"/>
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18 <output name="out_file1" file="concatenated.txt"/>
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19 </test>
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20 </tests>
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21
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22 <help>
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23 Background:
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24 This tool computationally predicts CTCF sites for a nucleotide sequence located on the reverse 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 last nucleotide sequence (separated by a tab). For example, if the sequence of interest is located on chromosome 3 with an ending genomic position of 1870000, the first line of the second input file must start with a fasta tag, and the second line will be chr3 1870000
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25
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26 Details of Algorithm:
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27 CTCF sites are predicted by applying the following equation
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28 w( ,j) = log2 (((f( ,j) + sqrt(N) x b( )) / (N + sqrt(N))) / b( ))
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29
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30 Where w( ,j) is the weight of nucleotide 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 .
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31
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32 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.
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33
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34
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35 Citation and further help: For further details of the algorithm, please refer to
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36
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37 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
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38
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39
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40 For queries/questions, email ucbtmaf@ucl.ac.uk
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41 </help>
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42
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43 </tool>
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