PssmIntermediateData

Defined in file scoremat.asn
C++ class: CPssmIntermediateData


PssmIntermediateData ::= SEQUENCE {

    -- observed residue frequencies (or counts) per position of the PSSM 
    -- (prior to application of pseudocounts)
    resFreqsPerPos              SEQUENCE OF INTEGER OPTIONAL, 

    -- Weighted observed residue frequencies per position of the PSSM.
    -- (N.B.: each position's weights should add up to 1.0).
    -- This field corresponds to f_i (f sub i) in equation 2 of 
    -- Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005.
    -- NOTE: this is needed for diagnostics information only (i.e.:
    -- -out_ascii_pssm option in psiblast)
    weightedResFreqsPerPos      SEQUENCE OF REAL OPTIONAL,

    -- PSSM's frequency ratios
    freqRatios                  SEQUENCE OF REAL,

    -- Information content per position of the PSSM
    -- NOTE: this is needed for diagnostics information only (i.e.:
    -- -out_ascii_pssm option in psiblast)
    informationContent          SEQUENCE OF REAL OPTIONAL,

    -- Relative weight for columns of the PSSM without gaps to pseudocounts
    -- NOTE: this is needed for diagnostics information only (i.e.:
    -- -out_ascii_pssm option in psiblast)
    gaplessColumnWeights        SEQUENCE OF REAL OPTIONAL,

    -- Used in sequence weights computation
    -- NOTE: this is needed for diagnostics information only (i.e.:
    -- -out_ascii_pssm option in psiblast)
    sigma                       SEQUENCE OF REAL OPTIONAL,

    -- Length of the aligned regions per position of the query sequence
    -- NOTE: this is needed for diagnostics information only (i.e.:
    -- -out_ascii_pssm option in psiblast)
    intervalSizes               SEQUENCE OF INTEGER OPTIONAL,

    -- Number of matching sequences per position of the PSSM (including the
    -- query)
    -- NOTE: this is needed for diagnostics information only (i.e.:
    -- -out_ascii_pssm option in psiblast)
    numMatchingSeqs             SEQUENCE OF INTEGER OPTIONAL,

    -- Number of independent observations per position of the PSSM
    -- NOTE: this is needed for building CDD database for DELTA-BLAST
    numIndeptObsr               SEQUENCE OF REAL OPTIONAL
}