Tag Archives: DNA

Parallelized computer code and DNA transcription

At stackexchange there is a super interesting discussion on parallelized computer code and DNA transcription (which is different to the DNA-based molecular programming literature…)

IF : Transcriptional activator; when present a gene will be transcribed. In general there is no termination of events unless the signal is gone; the program ends only with the death of the cell. So the IF statement is always a part of a loop.

WHILE : Transcriptional repressor; gene will be transcribed until repressor is not present.

FUNCTION: There are no equivalents of function calls. All events happen is the same space and there is always a likelihood of interference. One can argue that organelles can act as a compartment that may have a function like properties but they are highly complex and are not just some kind of input-output devices.

GOTO is always dependent on a condition. This can happen in case of certain network connections such as feedforward loops and branched pathways. For example if there is a signalling pathway like this: A → B → C and there is another connection D → C then if somehow D is activated it will directly affect C, making A and B dispensable.

Of course these are completely different concepts. I fully agree with the further stackexchange discussion that

it is the underlying logic that is important and not the statement construct itself and these examples should not be taken as absolute analogies. It is also to be noted that DNA is just a set of instructions and not really a fully functional entity … However, even being just a code it is comparable to a HLL [high level language] code that has to be compiled to execute its functions. See this post too.

Please forget everything you read from Francis Collins about this.

Is buccal DNA really buccal DNA?

This is an update of the recent TCRA post herewhere I argued that TCR studies shouldn’t be done with genomic DNA from peripheral blood cells. Instead, I was arguing for buccal DNA as epithelial cells will not have undergone somatic recombination. Only last week, however, I came across an earlier letter about DNA-based assessment of chimerism after allogeneic blood stem cell transplantation (BSCT). Continue reading Is buccal DNA really buccal DNA?

A man with a female DNA

Local newspapers just report a suicide – where the corpse had to be identified in the forensic department. Skin cells turned out to be male, blood cells to be female. The solution to this paradox was quite simple Continue reading A man with a female DNA


It might be fun to read here on a genetics board about DNA (Direct Note Access) which is a technology implemented in Melodyne that can extract notes from polyphonic music.
So far, it does not use a library of musical instruments according Peter Neubäcker, head of development, in an interview published in c’t 8/2008, p 34. It separates “musical content” defined by periodicity, similar overtones and meaningful musical distance like halftones. Although that’s something bioinformatics is trying for some while for DNA (desoxyribonucleic acid), I wonder if the decomposition concept in DNA would works also for DNA, yea, yea.

Annotation of regulatory sequences is largely insufficient

Of a proven set of regulatory regions in zebrafish, computer programs find only between 29% and 61% of the true motifs. This does not come very much unexpected given the vast array of data shown by the Encode project. It even relates to the most basic question: What is a gene?

The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.

iwith at least 5772 21U-RNAs? So – if I am sitting on the other side of the table when you are being examined don’t talk about junk DNA anymore, yea, yea.

What is DANN sequencing?

Did you ever came across DANN sequencing or plasmid DANN?

Here is my explanation: Native German MS WORD always corrects DNA to DANN (“then”). So if you don’t check your text, and your editor doesn’t check your text, and your reviewer doesn’t check your text – you will get an immortal entry in PUBMED like the guys below:


You may even earn money with typos

DNA data travel across Europe

heise.de reports that a top German politician wants to apply the Prüm contract also to the EU. The Prüm contract signed in May 2006 by Germany, France, Luxembourg, Netherlands, Austria and Spain regulates anti terror measurements and cross border prosecution of crimes. Mainstay of these activities are databases that allow the exchange of DNA and fingerprint data. Within the first 6 weeks of activity (as by November 2006) they report 1500 German hits in Austrian records (8 million inhabitants) and 1400 Austrian hits in German records (82 million inhabitants) if I understand that correctly. What does this now mean to have a German or a British or Swiss passport? For a respectable citizen and for a desperado?


5-2-07 update U.S.

6-3-07 update Germany

Allein im vergangenen Jahr nahmen die deutschen Polizeibehörden laut einer BKA-Statistik 72.280 Verdächtigen den genetischen Fingerabdruck ab, “immer häufiger auch bei eher geringfügigen Straftaten”, kritisiert Datenschützer Weichert.

A revival of DNA pooling

My interest in DNA pooling was always strong; we have developed methods doing this on the mass spec platform and applied it to the HLA region. I had, however, doubts if testing pools by less accurate methods like chip hybridization will work. The January issue of the AJHG now has a fascinating article how pooling may even work on the Affymetrix platform. Yea, yea.


DNA pooling can be even used in family context, see Wen Chung Lee in Cancer Epidemiology 2005 or Neil Risch in Genome Research 1998.

454 or 0815 or 4911

In a recent book chapter we discussed new genotyping and sequencing technologies. Our concluding remarks haven´t changed so much – it seems that realtime detection of single molecules is still not possible; micro electropheresis based methods have already reached their limit while sequencing by hybridization has severe restrictions when it comes to de novo (or re-) sequencing of whole genomes. At least for research purpose I expect that whole genome re-sequencing will replace current SNP based disease mapping. So far, sequencing by synthesis seems to be one of the few HT methods that already works at that scale. The 454 platform consists of 3 consecutive steps:

  1. DNA library preparation starts with genomic DNA (after fragmentation and adaptor ligation the single-stranded template DNA libraries are isolated and assessed (takes ~4 hours)
  2. sstDNA is emulsificated, then amplified and recovered on beads before sequencing primer are being annealed (takes 1 day)
  3. After washing, so called PicoTiterPlates are prepared and a process started that looks like a combination of pyrosequencing reaction, correct me if I am wrong, a pyrophospate dependent enzyme cascade emitting light being recorded by a CCD camera that watches each of the ~200,000 holes (takes ~6 hours according to a recent paper in GenomXPress 2/06, figures at 454.com)

With an average read length of 100 bp and 200,000 fragments (resulting in 20 Mb) in 6 hours, the throughput is about 60fold compared to Sanger sequencing. The recent Neanderthal paper raises five arguments why the 454 sequencing platform is extremely well suited for analyses of bulk DNA extracted from ancient remains.

  1. … it circumvents bacterial cloning, in which the vast majority of initial template molecules are lost during transformation and establishment of clones.
  2. … because each molecule is amplified in isolation from other molecules it also precludes template competition, which frequently occurs when large numbers of different DNA fragments are amplified together.
  3. … its current read length of 100–200 nucleotides covers the average length of the DNA preserved in most fossils.
  4. … it generates hundreds of thousands of reads per run, which is crucial because the majority of the DNA recovered from fossils is generally not derived from the fossil species, but rather from organisms that have colonized the organism after its death.
  5. … because each sequenced product stems from just one original single-stranded template molecule of known orientation, the DNA strand from which the sequence is derived is known. This provides an advantage over traditional PCR from double-stranded templates, in which the template strand is not known, because the frequency of different nucleotide misincorporations can be deduced … damage that affects different bases differently.

Except of the low read length most of these observations would benefit large scale resequencing projects in human individuals. My main point for starting ASAP resequencing projects: So far we have not achieved a dense resolution of the genome while deep resequencing project (for example at the CRP locus) got astonishing results. We do not even know what is going on in the “noncoding” regions. Finally deletions and CNVs have been largely neglected – another look at this question in the EJHG.
The question remains, what does 454 mean – my inquiry is still pending. As far as I know 0815 was a machine gun in World War I and is a synomym for something repeatedly boring while 4911 is a street number and stands for a perfume. Yea, yea.

Genetic code and God’s language -cont’d-

There is a new book by Francis Collins “The language of God“, one of the leading persons in human genome sequencing. As the commentary says:
Continue reading Genetic code and God’s language -cont’d-