Category Archives: Research


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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Solving problems in seconds

Sometimes a given solution to a problem lies much closer at hand than you expect. In my work I usually do the same task repeatedly with between 6 and 50 files. Even though Unix is very efficient in many ways, this still takes time to do by hand. I have thought of various ways around that problem, including using wildcards (*), but never got fully satisfied. But this week, I finally came up with the simplest solution this far. And it took about a minute or two to implement. I don’t know why I didn’t think about this a year ago. Maybe I thought that I would only do these repetitive tasks a couple of times. I was wrong, but thanks to Perl I can now be much more efficient (and write this instead of typing Unix commands…) The good thing about my implementation (in my opinion) is that it’s so flexible. Here’s my code, please comment if you feel that there is more efficient ways. “{}” is replaced by a number for each file name:


$versionID = "Version 1.0";
print "LoopCommand\n";
print "Version $versionID\n";
print "Written by Johan Bengtsson, October 2009\n";
print "-----------------------------------------\n";

print 'Execute command: ';
chomp($command = <STDIN>);
print 'From number: ';
chomp($start = <STDIN>);
print 'To number: ';
chomp($end = <STDIN>);

for ($i = $start ; $i <= $end ; $i++) {
$exec = $command;
$exec =~ s/\{\}/$i/g;
$result = `$exec`;
print $result;

Annika Dahlqvist – Enemy of logic and science?

Annika Dahlqvist, the doctor behind the LCHF diet (translation from Swedish Wikipedia), once again makes the front page of a Swedish tabloid (article in Swedish). This time, she has decided to battle the vaccination program for the Swine flu. However, the method she pleads for is so unbelievably stupid that one becomes scared.

In the Aftonbladet article, and repeated at her blog, Dahlqvist calls for cancellation of the vaccination program. The reasoning of this can be divided into three arguments:

  1. We know nothing about the side effects of the vaccine.
  2. It is a waste of money.
  3. If you eat according to the LCHF (Low carbohydrates, High fat) diet, your immune defense is so superior that the flu will be no problem.

Side effects?
The first statement is, at least partially, true. We do know very little about the side effects of a new vaccine. However, most often there are no to very small side effects of a vaccine. The rare reported serious side effects connected to earlier vaccines, such as paralysis, have been found to be caused by contaminated vaccine material. Since this happened, vaccine production methods have been greatly improved, and thus such cases no longer occurs.

Serious side effects aside, vaccines can have other side effects, just like all other medicines. Normal side effects are tiredness, stomach illness, dizziness etc. However, such conditions are much less serious than the flu itself, so they are not reason enough to turn down the vaccine. Like any other vaccine, the effectiveness of it will not be 100%. However, vaccines have proven to be a great way to deal with a variety of diseases which are now extinct, on the edge of extinction, or at least under control. Vaccines have proven to be much more effective than antibiotics in battling various diseases,as antibiotics many times causes bacterial resistance. Thus, it seems very arrogant to deny the effectiveness of vaccines against the swine flu.

Waste of money?
Given that you accept Annika Dahlqvist’s argument about diseases in general, it is of course a waste of money. Just like the vaccination programs against Poliomyelitis and Measles would be a waste of money, as they could have been cured by eating the right stuff. Personally, I am really happy to have these diseases out of the way. But if Dahlqvist really believes that we should not battle virus-related diseases, but rather try to live side-by-side with them, that’s up to her. Government paid vaccination programs can always be regarded a waste of money. That is more a matter of political views, not a rational argument against a vaccine.

Diet against flu?!
And now for the most ridiculous part of Dahlqvist argument. I mentioned in the previous paragraph how she thinks that eating “correctly” will give you a fantastic immune defense, capable of protecting from almost anything. This is so unbelievably stupid it seems like a joke. Sadly, it is not. She says exactly this in the article (my translation): “If you eat well, vitamin D and omega-3 you should have such a good infection defense you do not need to vaccinate yourself. We know that we get a much better infection defense by eating LCHF, low carb – high fat. We more seldom catch a cold and think we have a better defense in general. Many agree with me and others feel it is irresponsible to say something like this.”

The only rational part of this is the last sentence. Yes, it is irresponsible to say something like this. And a such statement makes it clear that you did not take the classes on virology during your education. And no scientist would believe this piece of crap. The sad part about it is that most people are not scientists or doctors, and have no way of knowing if she is right or not.

Let me explain something for you Annika: vitamin D and omega-3 does not protect you from viruses. Actually, no specific diet would. What protects you from viruses is hygiene, staying away from infected people (or rather, staying away from other people while you are infected and the first few days after the infection), and vaccines. This might sound unbelievable to you, but is common knowledge for anyone who has taken a course in microbiology or virology. When you say that you think that you have a better infection defense in general, that is exactly what you do. You think so. In reality, the only thing about LCHF that would give you a better immune defense system is placebo. Placebo is great, but advising people to rely on it is not only irresponsible – it is plain gambling with people’s lives without their knowledge. Any doctor would be cautious about such games, anyone except you. Shame on you, Annika Dahlqvist.

The hidden agenda
This leaves us with the following question; why does Dahlqvist want to gamble with people’s lives? This could be explained simply with stupidity, but as she as been proven to present a diet that apparently works (at least for many people) for weight loss, it is hard to put it off that easily. Instead, it seems that Dahlqvist wants to use the fear of the swine flu to agitate for a diet that was designed for diabetic patients. From being a decent doctor just a few years ago, Dahlqvist is now the leader of a group that looks increasingly like a sect. And this position makes her dangerous. She now has so many followers that would blindly do whatever she tells them. Like skipping the vaccination program to eat LCHF food instead. This battles the very core of the vaccination program.

Such battling places Dahlqvist, and the LCHF diet, in the same boat as other groups opposing the vaccination, such as Leonard Horowitz (that argues for silver ions, one of the most dangerous threats against antibiotics as they cause bacterial resistance) and Keith Scott Mumby (who argues that cancer can be cured by changing diet, don’t be surprised if Dahlqvist claims this next), making politics of a diet that should be regarded as… a diet. Both these “alternative doctors” have clear tendencies to defy science and common sense, using fear and unawareness to sell their own agendas.

Dahlqvist has previously shown to be sceptic against science in general, quoting from a recent Newsmill article (my tranlation): “At last, only the professors and the dietitians will remain to eat low fat – high carbohydrate diet. Then, maybe they will give in and admit the benefits of LCHF on health.” Beside attacking every scientist (!) and dietitian, Annika also forgets that science have infect given her diet some support, while it is rather society in general that has remained sceptical. However, it suits her role fighting the traditional sources of knowledge to turn against her previous allies. Probably she count on being accepted as a woman of the people, that got sacked for telling the truth. However, she is not telling the truth – and she was not sacked. She resigned herself.

It is rational to argue that vaccination should not be mandatory, but decisions should be based on facts, not on an agenda to sell cooking books. Yes – she writes cooking books about LCHF. And as she no longer is employed as a doctor, Dahlqvist has to sell books and lectures for her living. Of course she sees the opportunity. Let’s hope most people are clever enough to call the liar’s bluff.