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How to handle 2D protein sequences in HMMER?

ABC cdcer at hongkong.com
Fri Aug 29 13:29:37 EST 2003


I am now working on many 2nd protein sequences, I would like to ask if HMMER
possible to deal with them by default?

I just get the following error message when I build a model for a set of
aligned 2D protein sequences from CLUSTAL W.

===========================================================================
hmmbuild - build a hidden Markov model from an alignment
HMMER 2.3.1 (June 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment file:                    ../test.aln
File format:                       Clustal
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:                      test.profile
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Alignment:           #1
Number of sequences: 120
Number of columns:   973

WARNING: Looks like amino acid sequence, hope that's right
Determining effective sequence number    ... done. [1]
Weighting sequences heuristically        ... done.
Constructing model architecture          ...
FATAL: illegal state transition B->E in traceback
===========================================================================

But, anyway, I do not really understand the meaning of the error message.
Therefore, could you please direct me to somewhere that I could learn more of
the error messages.

Also, if there are  any working example to show how to change the default
alphabet setting in config.h and alphbet.c? Does above error relate to this
setting?

Thank you very much!
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