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Artikelaktionen

Bioinformatics & Systems Biology

Overview

Today, massively parallel DNA sequencing or hybridization approaches allow the identification of not only the gene repertoire but also the gene regulatory networks of an organism. The huge amounts of data acquired from such experiments can only be handled with intensive bioinformatics support that has to provide an adequate infrastructure for storing and analyzing these data. Thus, bioinformatics has to deliver efficient data analysis algorithms, user-friendly tools and software applications, as well as extensive hardware infrastructure for answering such questions.

As part of the Bielefeld-Giessen Resource Center for Microbial Bioinformatics (BiGi), a service unit of the 'German Network for Bioinformatics Infrastructure – de.NBI', the group is focused on data management for genome and post-genome research projects that require new software solutions for systematic data acquisition, secure data storage of structured information, and high-throughput data analysis. Bioinformatics training and education and the cooperation within the German bioinformatics community is a main scope of the group.

Recent publications
Plasmids play a vital role in the environmental adaptation of bacteria. Due to potential mobilization or conjugation capabilities, they are important genetic vehicles for antimicrobial resistance genes and virulence factors with huge clinical implications. To comprehensively characterize plasmids via NGS methods, Platon allows the identification and characterization of plasmid-borne contigs from bacterial short-read draft assemblies achieving both high accuracy and balanced classifications in terms of sensitivity and specificity. The software follows a new approach to this problem exploiting the natural distribution bias of protein-coding genes between chromosomes and plasmids represented by a new metric: the replicon distribution score (RDS). To further increase the achieved sensitivity, platon applies several heuristics taking into account plasmid-specific contig characterizations.
Bacterial whole-genome sequencing has become daily routine in many fields. Technical advances and dropping costs have resulted in a tremendous increase in available sequence data. However, the comprehensive in-depth analysis thereof remains an arduous and time-consuming task. Here, we introduce ASA³P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline conducts necessary raw data processing steps as well as comprehensive genome characterizations, e.g. taxonomic classification, detection of AMR genes and virulence factors and much more. The workflow is implemented in a fully-automatic manner, scaling from tiny to very large cohorts via a portable Docker image or a highly-scalable cloud version. All results are presented via interactive HTML reports.
Software
The huge amounts of data acquired from PolyOmics technologies can only be handled with intensive bioinformatics support that has to provide an adequate data management, efficient data analysis algorithms, and user-friendly software applications. Over the last years, we developed a large scale software suite to substantially support researchers in the field of genome and metagenome, transcriptome, proteome, and metabolome data analysis. As all software applications follow a similar design pattern, experimental data as well as analysis results can be easily integrated to achieve higher-level evaluation and combined visualizations.
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