REDUCE Suite

AffinityProfile is designed to scan a sequence file against a list of PSAMs or IUPAC motifs to get single base resolution affinity profiles. For convenience, it also allows for a single PSAM (-psam=one_PSAM_file) or an IUPAC motif (-motif=one_IUPAC_motif) to be specified directly on the command line. The PSAMs can be from a MatrixREDUCE or MotifREDUCE run, or a collection of pseudo-PSAMs from literature (as in $REDUCE_SUITE/data/PSAMs/ directory).

AffinityProfile [options] -sequence=seqfile \
                         -psam=one_PSAM_file | -psam_list=list_of_PSAMs |
                         -motif=one_IUPAC_motif | -motif_list=list_of_motifs

  Required parameters:
    -sequence=file_name  --- name of sequence file in FASTA format
    -psam=one_PSAM_file    --- file name of one PSAM
    -psam_list=list_of_PSAMs --- file name containing a list of PSAMs
    -motif=IUPAC_motif     --- one IUPAC motif
    -motif_list=list_of_motifs --- file name containing a list of IUPAC motifs

  Optional parameters:
    [-threshold=float]   --- threshold of affinity for output (0.0)
    [-output=dir_name]   --- path to the output directory (./)
    [-prefix=string]     --- prepended to output profile name (aff_)
    [-affsum=string]     --- file of total affinity per sequence (seq_psam.dat)
    [-detail]            --- also output detailed affinity along each sequence
    [-ids=string]        --- a ',' or ';' delimited list of IDs
    [-column]            --- used with -ids, set profile column-wise for each id
    [-normalize]         --- linear re-scale (per PSAM) the maximum profile to 1.0
    [-strand=integer]      ---  1 |+1 |F | L for leading strand;
                                2 |+2 |B     for both strands;
                               -1 | R |C     for reverse complementary;
                                   with -motif, default to leading strand
                                   with -psam, default to PSAM setting

  Usage:
      (1) AffinityProfile -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
                          -psam_list=psams.list
      (2) AffinityProfile -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
                          -motif=aaaccct
      (3) AffinityProfile -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
                          -motif=aaaga -ids='YAL001C;YAL002W' -column

Notes:

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• By default, the reported affinities take into account of the threshold (default to 0) specified on the command-line. Thus, per slide window, if the affinity is less than the threshold, it will neither be outputted per window nor added into the sum per sequence (as in file seq_psam_thr.dat, see below).
• AffinityProfile also outputs two files with fixed names: seq_psam.dat (which sums up all affinities, even those below threshold, for reference and comparison) and seq_psam_thr.dat (taking into account of threshold) that contain the sum of affinities per sequence in a tab-delimited format that can be fed directly into Transfactivity.
• Following each run of MatrixREDUCE or MotifREDUCE, two fix-named files, psams.list and motifs.list, are also available, which can be fed into AffinityProfile, as shown in the first example above.
• This is yet another example illustrating how the REDUCE Suite has been designed with tools that are seamlessly inter-connected to allow for great flexibility.