PssmFinalData

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


PssmFinalData ::= SEQUENCE {

    -- PSSM's scores
    scores              SEQUENCE OF INTEGER, 

    -- Karlin & Altschul parameter produced during the PSSM's calculation
    lambda              REAL,

    -- Karlin & Altschul parameter produced during the PSSM's calculation
	kappa               REAL,

    -- Karlin & Altschul parameter produced during the PSSM's calculation
    h                   REAL,

    -- scaling factor used to obtain more precision when building the PSSM.
    -- (i.e.: scores are scaled by this value). By default, PSI-BLAST's PSSM
    -- engine generates PSSMs which are not scaled-up, however, if PSI-BLAST is
    -- given a PSSM which contains a scaled-up PSSM (indicated by having a
    -- scalingFactor greater than 1), then it will scale down the PSSM to
    -- perform the initial stages of the search with it.
    -- N.B.: When building RPS-BLAST databases, if formatrpsdb is provided 
    -- scaled-up PSSMs, it will ensure that all PSSMs used to build the 
    -- RPS-BLAST database are scaled by the same factor (otherwise, RPS-BLAST 
    -- will silently produce incorrect results).
    scalingFactor       INTEGER DEFAULT 1,

    -- Karlin & Altschul parameter produced during the PSSM's calculation
    lambdaUngapped      REAL OPTIONAL,

    -- Karlin & Altschul parameter produced during the PSSM's calculation
	kappaUngapped       REAL OPTIONAL,

    -- Karlin & Altschul parameter produced during the PSSM's calculation
    hUngapped           REAL OPTIONAL,

    -- Word score threshold
    wordScoreThreshold    REAL OPTIONAL
}