4,554 research outputs found
Fine-tuning structural RNA alignments in the twilight zone
No full textBremges A, Schirmer S, Giegerich R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 2010;11(1): 222.Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index
Assembling the microbial dark matter
No full textBremges A. Assembling the microbial dark matter. Bielefeld: Universität Bielefeld; 2016.The vast majority of microbial species found in nature has yet to be grown in pure culture, turning metagenomics and – more recently – single cell genomics into indispensable methods to study the microbial dark matter.
I developed, applied, and benchmarked genome assembly protocols for single cell and metagenome sequencing data to access microbial dark matter genomes.
In the first part of my thesis, I propose new algorithms that naturally exploit the complementary nature of single cells and metagenomes to improve the quality of single cell assemblies.
In the second part, I apply advanced metagenome assembly and binning techniques to untangle genomes from metagenomes, eventually reconstructing hundreds of near-complete genomes of process-relevant community members in the biogas microbiome
Stylos kai edraiōma tēs ekklēsias, sive, Dissertatio de iustificatione hominis
No full textquam ... sub praesidio ... Ioh. Henrici Heideggeri ... placido eruditorum examini subiicit Andreas Steinerus, Vitod. author & respondens, ad diem Octobris loco horisque solitisDiss. Hohe Schule Zürich, 167
MeCorS: Metagenome-enabled error correction of single cell sequencing reads
No full textBremges A, Singer E, Woyke T, Sczyrba A. MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics. 2016;32(14):2199-2201.UNLABELLED: We present a new tool, MeCorS, to correct chimeric reads and sequencing errors in Illumina data generated from single amplified genomes (SAGs). It uses sequence information derived from accompanying metagenome sequencing to accurately correct errors in SAG reads, even from ultra-low coverage regions. In evaluations on real data, we show that MeCorS outperforms BayesHammer, the most widely used state-of-the-art approach. MeCorS performs particularly well in correcting chimeric reads, which greatly improves both accuracy and contiguity of de novo SAG assemblies.
AVAILABILITY AND IMPLEMENTATION: https://github.com/metagenomics/MeCorS
CONTACT: [email protected]
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
The Author 2016. Published by Oxford University Press
Bioboxes: standardised containers for interchangeable bioinformatics software
No full textBelmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD. Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience. 2015;4(1): 47.Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable
Author: Andreas Johannis Prytz
No full textAn edition of the consecration sermons in Gothenburg Cathedral 1633 by Superintendent Andreas Johannis Prytz, with introductory comments. The first sermon deals with the need for Church buildings, the second with the consecration of a new Church
We must combine conservation of nature with benefits to society. Interview by Gaby Allheilig with Andreas Heinimann on IPBES' Global Assessment Report on Biodiversity and Ecosystem Services
No full textOn 6 May 2019, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) presented its report on the state of biodiversity and ecosystem services worldwide. The first such assessment since 2005, it concludes that biodiversity and ecosystem loss has reached the point where it threatens human well-being. The researchers involved recommend several urgent measures to political decision-makers. Andreas Heinimann of CDE was the one Swiss scientist who worked as a lead author on a chapter of the report
To athanaton tēs psychēs, sive, Dissertatio de animae immortalitate, ex naturae & sanae rationis lumine demonstrata
No full textquam ... sub praesidio ... Iohannis Lavateri ... publicae ac placidae disquisitioni submittit Andreas Steinerus, Vitod. author & respondens ...Dedikation an Johannes Lavater, Jacob Meyer, Joh. Jacob Schaedler und Jacob Hegner auf dem Titelbl. versoDiss. Hohe Schule Zürich, 167
Haploflow: strain-resolved de novo assembly of viral genomes
No full textFritz A, Bremges A, Deng Z-L, et al. Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biology. 2021;22(1): 212
Family Virtues and Social Critique: Andreas Latzko’s Anti-War Prose (1917-1918)
No full textBetween 1917 and 1918, the Austro-Hungarian author Andreas Latzko (1876-1943) wrote three separate publications against the Great War: Menschen im Krieg (1917), Friedensgericht (1918), and Der letzte Mann (published 1919). Literary historians tend to bypass these works, and the few who note them chiefly focus on the best-selling novella cycle Menschen im Krieg (1917). It is usually presented as an example of expressionist political prose, or as a mixture of social satire and aesthetic shock-tactics that chiefly remains indebted to realist traditions, albeit with occasional incursions into expressionistic styles..
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