# HG changeset patch
# User mkhan1980
# Date 1362397133 18000
# Node ID 5f235b95619fbacd5ecb8c5e3c5ede0890b90198
# Parent  2cceb9398d33bb8c32c4892ee5d9edc1da9f2918
Uploaded

diff -r 2cceb9398d33 -r 5f235b95619f check2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check2.xml	Mon Mar 04 06:38:53 2013 -0500
@@ -0,0 +1,43 @@
+    <tool id="fa_gc_content_2" name="Discover CTCF Sites for Reverse Strand">
+      <description></description>
+      <command interpreter="perl">check2.pl $input $input2 $output</command>
+      <inputs>
+        <param format="fasta" name="input" type="data" label="Reverse Strand Sequence File"/>
+ <param format="fasta" name="input2" type="data" label="Reverse Strand Coordinate file"/>
+      </inputs>
+
+
+      <outputs>
+      <data format="tabular" name="output" />
+    </outputs>
+  
+    <tests>
+      <test>
+        <param name="input" value="fa_gc_content_input3.fa"/>
+        <param name="input2" value="fa_gc_content_input4.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 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
+
+Details of Algorithm:
+CTCF sites are predicted by applying the following equation
+w( ,j) = log2 (((f( ,j) + sqrt(N) x b( )) / (N + sqrt(N))) / b( ))
+
+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  . 
+
+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>