Tag Archives: HMMER

HMMER3 released – with a pre-compiled binary!

As I have recently complained about open source software coming without pre-compiled binaries, I salute the release of HMMER beta 3, which has a pre-compiled Intel/Linux tar-ball. This is exactly the kind of convenience measures I have asked for, and thus I wanted to state that clearly here. Well done, Sean Eddy and company!

HMMER is a bioinformatics software for finding sequence homology. People into bioinformatics may appreciate some of the new features, like multicore support, and better-than-BLAST speeds (unbelievable but true!). For those of you that are interested, the full range of features, as well as the software download can be found here:

HMMER 3.0b3: the final beta test release

An unusual error?

I just ran into a problem using HMMER, where it aborts the building of an HMM-profile (using hmmbuild) with this line: “FATAL: illegal state transition B->E in traceback” Is there anyone who has seen this HMMER error before? Anyone who know what it means and/or how to solve it? Please let me know as soon as possible.

hmmbuild - build a hidden Markov model from an alignment
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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Alignment file: alignment1.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: alignment1.hmm
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Alignment: #1
Number of sequences: 5517
Number of columns: 2305

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