General Category => Documentation => Topic started by: xiangjun on September 29, 2016, 12:41:18 pm

Title: OptimizePSAM
Post by: xiangjun on September 29, 2016, 12:41:18 pm
This program performs a single point optimization of either an initial (pseudo-) PSAM or a seed motif against the measurement file and sequence. Internally, it uses exactly the same Levenberg-Marquardt non-linear least squares fitting algorithm as in MatrixREDUCE (

OptimizePSAM [options] -sequence=seqfile -measurement=measfile \
                       -psam=PSAM_file | -motif=IUPAC_Motif

  Required parameters:
    -sequence=file_name    --- name of a FASTA sequence file
    -meas=measfile         --- measurement (expression/binding) file in tab-delimited format
    -psam=PSAM_file        --- PSAM file to be optimized
    -motif=seed_motif      --- Seed IUPAC motif sequence to be optimized

  Optional parameters:
    [-output=dir_name]     --- path to the output directory (./)
    [-p_value=float]       --- threshold to decide if optimized PSAM is significant (0.001)
    [-filename=file]       --- name of the optimized PSAM
    [-strand=integer]      ---  1 |+1 |F | L for leading strand (1);
                                2 |+2 |B     for both strands;
                               -1 | R |C     for reverse complementary;
                                0 | A |D     auto-detection (check 1 and 2)
                           --- direct running diagnostics message to stderr,
                               stdout or a file (stderr)
    [-help]                --- print out this help message

    OptimizePSAM \
       -measurement=$REDUCE_SUITE/data/mRNA_expression/Spellman1998AlphaTimeCourse.tsv \
       -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
       -motif=ACGCGT -file=ACGCGT.psam