[Bio-software] HMMER illegal transitions

Kathryn E. Bushley via bio-soft%40net.bio.net (by keb45 At cornell.edu)
Sun Nov 19 11:53:23 EST 2006


Hello,

I'm trying to build and hmm model and keep getting the following error...

hmmbuild - build a hidden Markov model from an alignment
HMMER 2.2g (August 2001)
Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment file:                    FgramIter2coded.phy
File format:                       SELEX
Search algorithm configuration:    Multiple domain (hmmls)
Model construction strategy:       MAP (gapmax hint: 0.50)
Null model used:                   (default)
Prior used:                        (default)
Sequence weighting method:         G/S/C tree weights
New HMM file:                      FgramIter2.hmm
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Alignment:           #1
Number of sequences: 715
Number of columns:   57

Determining effective sequence number    ... done. [1]
Weighting sequences heuristically        ... done.
Constructing model architecture          ...
FATAL: illegal state transition B->E in traceback

Assuming this has something to do with the protein alphabet or transition
matrix...can anyone direct me to resources for fixing this problem?

thanks,

kathryn bushley


Kathryn E. Bushley
PhD Candidate
Cornell University
Department of Plant Pathology
334 Plant Science Bldg, Tower Road
Ithaca, NY 14853
(607) 539-6285

"He who wonders discovers that this in itself is wonder"  M.C. Escher



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