Alla Mikheenko

MetaQUAST: evaluation of metagenome assemblies

UNLABELLED During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets. AVAILABILITY AND IMPLEMENTATION http://bioinf.spbau.ru/metaquast CONTACT aleksey.gurevich@spbu.ru SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Dereplication of peptidic natural products through database search of mass spectra

Peptidic Natural Products (PNPs) are widely used compounds that include many antibiotics and a variety of other bioactive peptides. While recent breakthroughs in PNP discovery raised the challenge of developing new algorithms for their analysis, identification of PNPs via database search of tandem mass spectra remains an open problem. To address this problem, natural product researchers utilize dereplication strategies that identify known PNPs and lead to the discovery of new ones even in cases when the reference spectra are not present in existing spectral libraries. DEREPLICATOR is a new dereplication algorithm that enabled high-throughput PNP identification and that is compatible with large-scale mass spectrometry-based screening platforms for natural product discovery. After searching nearly one hundred million tandem mass spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure, DEREPLICATOR identified an order of magnitude more PNPs (and their new variants) than any previous dereplication efforts.

Icarus: visualizer for de novo assembly evaluation

: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. AVAILABILITY AND IMPLEMENTATION http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.

A circuit synthesis technique based on network determinant expansion

In this paper we present a simple technique of analog electronic circuits synthesis by means of a linear representation. The approach is based on generalized parameter extraction method. It describes the procedure for developing the circuit topology both for passive or active circuits. The input data for the proposed synthesis method are the arbitrary network function approximated in polynomial form and specified elements set. In contrast to other synthesis approaches the proposed technique provides the realization of full set of equivalent circuits and allow to choose the best circuit solutions by various criteria. Experiments conducted on the low-pass filter design demonstrate the simplicity and effectiveness of synthesis method.

Versatile genome assembly evaluation with QUAST-LG

Motivation The emergence of high‐throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long‐read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian‐size genomes. Results In this manuscript, we demonstrate performance of the state‐of‐the‐art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST‐LG—a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST‐LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference. Availability and implementation http://cab.spbu.ru/software/quast‐lg

Dereplication of microbial metabolites through database search of mass spectra

Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.New natural products can be identified via mass spectrometry by excluding all known ones from the analysis, a process called dereplication. Here, the authors extend a previously published dereplication algorithm to different classes of secondary metabolites.

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that include many antibiotics and a variety of other bioactive compounds. While recent breakthroughs in RiPP discovery raised the challenge of developing new algorithms for their analysis, peptidogenomic-based identification of RiPPs by combining genome/metagenome mining with analysis of tandem mass spectra remains an open problem. We present here MetaRiPPquest, a software tool for addressing this challenge that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just six genomic and metagenomic datasets, MetaRiPPquest identified 27 known and discovered 5 novel RiPP natural products.

Using Parameters of Protein Oxidative Modifications for Differential Diagnosis of Progressive Ovarian Cancer

Background: The aim of the study was to elaborate a method of specific diagnostics of progressive ovarian cancer. Methods and Findings: We observed 21 parameters in plasma of 300 primary ovarian cancer patients, stage III and IV. Using the least squares method, approximation of the relative frequencies by the Rayleigh distribution density was conducted for each parameter. The likelihood functions were constructed and intervals for each measurement on each stage were determined. Approximation accuracy was identified while checking the hypothesis of correspondence of parameter practical value to the theoretical law of density distribution by Pearson criterion. Conclusions: The obtained results suggest that the level of the oxidative modification of proteins may serve as a reliable indicator for the differential diagnosis of stages III and IV ovarian cancer.