Kaiserslautern University of Technology

About: Kaiserslautern University of Technology is a education organization based out in Kaiserslautern, Rheinland-Pfalz, Germany. It is known for research contribution in the topics: Laser & Population. The organization has 8881 authors who have published 19452 publications receiving 434955 citations.

VSEARCH: a versatile open source tool for metagenomics

Abstract: Background: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results: VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion: VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.

Electromagnetically induced transparency : Optics in coherent media

Abstract: Coherent preparation by laser light of quantum states of atoms and molecules can lead to quantum interference in the amplitudes of optical transitions. In this way the optical properties of a medium can be dramatically modified, leading to electromagnetically induced transparency and related effects, which have placed gas-phase systems at the center of recent advances in the development of media with radically new optical properties. This article reviews these advances and the new possibilities they offer for nonlinear optics and quantum information science. As a basis for the theory of electromagnetically induced transparency the authors consider the atomic dynamics and the optical response of the medium to a continuous-wave laser. They then discuss pulse propagation and the adiabatic evolution of field-coupled states and show how coherently prepared media can be used to improve frequency conversion in nonlinear optical mixing experiments. The extension of these concepts to very weak optical fields in the few-photon limit is then examined. The review concludes with a discussion of future prospects and potential new applications.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Abstract: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence. le formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.