EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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phmmer assigns incorrect scores to degenerate residues #104

Closed traviswheeler closed 7 years ago

traviswheeler commented 7 years ago

ID h94 TITLE phmmer assigns incorrect scores to degenerate residues AFFECTS 3.0 FIXED_IN 3.1b1 STATUS CLOSED XREF SRE:J9/87; svn r3878 REPORTED_BY Elena Rivas OPENED_DATE SRE, 25 Feb 2012 CLOSED_DATE SRE, 25 Feb 2012 DESCRIPTION
When converting joint probs p_ab to conditionals p(b|a), p7builder{Load,Set}ScoreSystem() were only converting K canonical residues, and leaving the degenerate residues as joints. Degenerate residue scores were therefore incorrect, and highly penalized.