EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
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traces containing X (fragments) are misaligned #74

Closed traviswheeler closed 7 years ago

traviswheeler commented 7 years ago

ID h64 TITLE traces containing X (fragments) are misaligned AFFECTS 3.0b2 and earlier FIXED_IN 3.0b3 STATUS CLOSED XREF J5/105 REPORTED_BY Elena Rivas OPENED_DATE 6 Nov 2009 CLOSED_DATE SRE, Thu Nov 12 08:34:23 2009 DESCRIPTION
Core traces from model construction involving fragments may result in B->X->{MDI}k and {MDI}k->X->E entry/exit transitions, not just B->X->Mk and Mk->X->E. Elena saw one bug having to do with X state handling in p7_tracealign_MSA(). There were in fact several bugs, there and elsewhere. The problem has not manifested itself in any bug reports yet. If it did, it would manifest as odd placement of N/C terminal residues in hmmbuild -O resaved alignments.