the only example of this I have at the moment is with respect to the new gene families defined on lis-dev, but I suspect it occurs elsewhere without my having noticed it.
Compare : repeat algorithm
/lis_context_viewer/#/search/lis/glyma.Glyma.08G224600?neighbors=15&sources=lis&matched=4&intermediate=5&algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=40®exp=medtr&order=chromosome&alpha=0.85&kappa=10&minsup=2&minsize=5
to : smith waterman
/lis_context_viewer/#/search/lis/glyma.Glyma.08G224600?neighbors=15&sources=lis&matched=4&intermediate=5&algorithm=smith-waterman&match=10&mismatch=-1&gap=-1&score=30&threshold=40®exp=medtr&order=chromosome&alpha=0.85&kappa=10&minsup=2&minsize=5
with respect to the genes in the family that is the "focus". one of the medtr copies (Medtr4g005390) seems to disappear altogether from the alignment (can't even find it in the list of genes given in the track slider, so it must not just be a question of "optics"...)
the only example of this I have at the moment is with respect to the new gene families defined on lis-dev, but I suspect it occurs elsewhere without my having noticed it.
Compare : repeat algorithm /lis_context_viewer/#/search/lis/glyma.Glyma.08G224600?neighbors=15&sources=lis&matched=4&intermediate=5&algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=40®exp=medtr&order=chromosome&alpha=0.85&kappa=10&minsup=2&minsize=5 to : smith waterman /lis_context_viewer/#/search/lis/glyma.Glyma.08G224600?neighbors=15&sources=lis&matched=4&intermediate=5&algorithm=smith-waterman&match=10&mismatch=-1&gap=-1&score=30&threshold=40®exp=medtr&order=chromosome&alpha=0.85&kappa=10&minsup=2&minsize=5
with respect to the genes in the family that is the "focus". one of the medtr copies (Medtr4g005390) seems to disappear altogether from the alignment (can't even find it in the list of genes given in the track slider, so it must not just be a question of "optics"...)