Motivation: RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information. Results: We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are ‘energetically favorable’. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated accurately and efficiently for RNA molecules well beyond the length range accessible to enumerative algorithms. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html . Contact:qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact:qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online.

Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2-6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays. We propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases, and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated data sets and on data sets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these data sets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases. Dante is open source software, freely available for download at https://github.com/jbudis/dante Supplementary data are available at Bioinformatics online.

Summary: This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture‐dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left‐hand palm, left‐hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture‐dependent and culture‐independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum , Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous ‘mummy pathogens’. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd

Copy number variants (CNVs) are an important type of human genome variation, which play a significant role in evolution contribute to population diversity and human genetic diseases. In recent years, next generation sequencing has become a valuable tool for clinical diagnostics and to provide sensitive and accurate approaches for detecting CNVs. In our previous work, we described a non-invasive prenatal test (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA for detection of CNV aberrations ≥600 kbp. We reanalyzed NIPT genomic data from 5018 patients to evaluate CNV aberrations in the Slovak population. Our analysis of autosomal chromosomes identified 225 maternal CNVs (47 deletions; 178 duplications) ranging from 600 to 7820 kbp. According to the ClinVar database, 137 CNVs (60.89%) were fully overlapping with previously annotated variants, 66 CNVs (29.33%) were in partial overlap, and 22 CNVs (9.78%) did not overlap with any previously described variant. Identified variants were further classified with the AnnotSV method. In summary, we identified 129 likely benign variants, 13 variants of uncertain significance, and 83 likely pathogenic variants. In this study, we use NIPT as a valuable source of population specific data. Our results suggest the utility of genomic data from commercial CNV analysis test as background for a population study.

The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion.