Manual for TFBS-Scanner

● Manual Reference Pages - TFBS-Scanner V1.0

1. NAME

   TFBS-Scanner - Program for Scanning Transcription Factor Binding Sites

2. SYNOPSIS

   [result, fid1, fid2] = tfbs_scanner('test_input.xlsx', 'test_output', 'excel', scanner_threshold, pwmcluster);

3. DESCRIPTION

   TFBS-Scanner is a computational tool for predicting TFBSs based on TRANSFAC 7.0 Public 2005 library.
   It requires MATLAB with Bioinformatics toolbox.

4. COMMANDS AND OPTIONS
   [RESULT, FID1, FID2] = tfbs_scanner(FINPUT, FOUTPUT, FINPUTTYPE, SCANNER_THRESHOLD, PWMCLUSTER);

   OPTIONS:
   FINPUT: input file name
   FOUTPUT: output file name
   FINPUTTYPE: 'fasta' (FASTA format) or 'excel' (EXCEL FILE, see test_input.xlsx for this format)
   SCANNER_THRESHOLD: 0 ~ 1 (we recommend 0.1)
   PWMCLUSTER: 1 (PWMCLUSTERTYPE1), 2 (PWMCLUSTERTYPE2), 3 (PWMCLUSTERTYPE3)

   OUTPUTS:
   RESULT: MATLAB structure variable
   RESULT(i).score_array(j).S(k): the start site of the kth TFBS of the jth PWM Cluster of the ith sequence
   RESULT(i).score_array(j).F(k): the end site of the kth TFBS of the jth PWM Cluster of the ith sequence
   RESULT(i).score_array(j).W(k): the score of the kth clustered TFBS of the jth PWM Cluster of the ith sequence
   RESULT(i).score_array(j).S(k): the number of clustered TFBSs (PWM) of the kth TFBS of the jth PWM Cluster of the ith sequence

   RESULT(i).gene_result.Result(j).plusStart(k): the start site (plus strand) of the kth TFBS of the jth PWM of the ith sequence
   RESULT(i).gene_result.Result(j).plusEnd(k): the end site (plus strand) of the kth TFBS of the jth PWM of the ith sequence   
   RESULT(i).gene_result.Result(j).plusQsel(k): the score (plus strand) of the kth TFBS of the jth PWM of the ith sequence
   RESULT(i).gene_result.Result(j).minusStart(k): the start site (minus strand) of the kth TFBS of the jth PWM of the ith sequence
   RESULT(i).gene_result.Result(j).minusEnd(k): the end site (minus strand) of the kth TFBS of the jth PWM of the ith sequence 
   RESULT(i).gene_result.Result(j).minusQsel(k): the score (minus strand) of the kth TFBS of the jth PWM of the ith sequence
   

   FID1: file identifier of the first output file (PWM) If failed, FID1 = -1
   FILE NAME: FOUTPUT_PWM_GENESYMBOL.TXT
   COLUMN1: GENESYMBOL
   COLUMN2: TFBS-Scanner (FIXED)
   COLUMN3: PWM (FIXED)
   COLUMN4: TFBS start site
   COLUMN5: TFBS end site
   COLUMN6: subsequence
   COLUMN7: strand information
   COLUMN8: TFBS affinity score
   COLUMN9: PWM ID

   FID2: file identifier of the second output file (PWMCluster) If failed, FID1 = -1
   FILE NAME: FOUTPUT_PWMCluster_GENESYMBOL.TXT
   COLUMN1: GENESYMBOL
   COLUMN2: TFBS-Scanner (FIXED)
   COLUMN3: PWM (FIXED)
   COLUMN4: TFBS start site
   COLUMN5: TFBS end site
   COLUMN6: subsequence
   COLUMN7: +/- (FIXED)
   COLUMN8: TFBS affinity score
   COLUMN9: PWMCluster ID