Context dependency of nucleotide probabilities and variants in human DNA.

BACKGROUND: Genomic DNA has been shaped by mutational processes through evolution. The cellular machinery for error correction and repair has left its marks in the nucleotide composition along with structural and functional constraints. Therefore, the probability of observing a base in a certain position in the human genome is highly context-dependent. RESULTS: Here we develop context-dependent nucleotide models. We first investigate models of nucleotides conditioned on sequence context. We develop a bidirectional Markov model that use an average of the probability from a Markov model applied to both strands of the sequence and thus depends on up to 14 bases to each side of the nucleotide. We show how the genome predictability varies across different types of genomic regions. Surprisingly, this model can predict a base from its context with an average of more than 50% accuracy. For somatic variants we show a tendency towards higher probability for the variant base than for the reference base. Inspired by DNA substitution models, we develop a model of mutability that estimates a mutation matrix (called the alpha matrix) on top of the nucleotide distribution. The alpha matrix can be estimated from a much smaller context than the nucleotide model, but the final model will still depend on the full context of the nucleotide model. With the bidirectional Markov model of order 14 and an alpha matrix dependent on just one base to each side, we obtain a model that compares well with a model of mutability that estimates mutation probabilities directly conditioned on three nucleotides to each side. For somatic variants in particular, our model fits better than the simpler model. Interestingly, the model is not very sensitive to the size of the context for the alpha matrix. CONCLUSIONS: Our study found strong context dependencies of nucleotides in the human genome. The best model uses a context of 14 nucleotides to each side. Based on these models, a substitution model was constructed that separates into the context model and a matrix dependent on a small context. The model fit somatic variants particularly well.

Context dependent prediction in DNA sequence using neural networks.

One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.

GISA: using Gauss Integrals to identify rare conformations in protein structures.

The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a "fingerprint of topological-geometric values" consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains. This allows fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds. Applying GISA to sets of several thousand high resolution structures, we first show how the most basic Gauss integral, the writhe, enables swift identification of pre-defined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, an application of the basic scan method in GISA's tool-box revealed 10 known cases of knots as the top positive writhe cases, while placing at the top of the negative writhe 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed. Possible general applications of GISA are fold classification and structural alignment based on local Gauss integrals. Others include finding errors in protein models and identifying unusual conformations that might be important for protein folding and function. By its broad potential, we believe that GISA will be of general benefit to the structural bioinformatics community. GISA is coded in C and comes as a command line tool. Source and compiled code for GISA plus read-me and examples are publicly available at GitHub (https://github.com).