ID h74
TITLE Different envelopes, identical alignment
AFFECTS 3.0b3 and earlier
FIXED_IN 3.0rc1
STATUS CLOSED
XREF J5/130; notebook/1222-hmmer-bug-h74
REPORTED_BY Craig McAnulla craigm@ebi.ac.uk, 26 Nov 2009
OPENED_DATE SRE, Tue Dec 22 15:36:03 2009
CLOSED_DATE
DESCRIPTION
Rarely, two different (overlapping) envelopes can produce the
same OA alignment.
McAnulla's example is the Pfam_B model Pfam-B_9291 against
Uniparc UPI0000022264.
Implemented workaround_bug_h74() in p7_tophits.c. This hides all but
one envelope containing a duplicate alignment.
A better fix is to define envelope by profile endpoints in addition
to sequence endpoints, revise rescore_isolated_domain() to take
profile endpoints into account, and write versions of Forward and
Backward that limit the calculation to an envelope on the profile.
Defer this to future.
ID h74 TITLE Different envelopes, identical alignment AFFECTS 3.0b3 and earlier FIXED_IN 3.0rc1 STATUS CLOSED XREF J5/130; notebook/1222-hmmer-bug-h74 REPORTED_BY Craig McAnulla craigm@ebi.ac.uk, 26 Nov 2009 OPENED_DATE SRE, Tue Dec 22 15:36:03 2009 CLOSED_DATE
DESCRIPTION
Rarely, two different (overlapping) envelopes can produce the same OA alignment.
McAnulla's example is the Pfam_B model Pfam-B_9291 against Uniparc UPI0000022264.
Implemented workaround_bug_h74() in p7_tophits.c. This hides all but one envelope containing a duplicate alignment.
A better fix is to define envelope by profile endpoints in addition to sequence endpoints, revise rescore_isolated_domain() to take profile endpoints into account, and write versions of Forward and Backward that limit the calculation to an envelope on the profile. Defer this to future.