Search results for "alignment"
showing 10 items of 627 documents
Multiple Protein Sequence Alignment with MSAProbs
2013
Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact approach to producing optimal multiple alignments, the majority of state-of-the-art MSA algorithms are designed based on the progressive alignment heuristic. In this chapter, we outline MSAProbs, a parallelized MSA algorithm for protein sequences based on progressive alignment. To achieve high alignment accuracy, this algorithm employs a hybrid combination of a pair hidden Markov model and a partition function to calculate posterior…
Complete subunit sequences, structure and evolution of the 6 x 6-mer hemocyanin from the common house centipede, Scutigera coleoptrata.
2003
Hemocyanins are large oligomeric copper-containing proteins that serve for the transport of oxygen in many arthropod species. While studied in detail in the Chelicerata and Crustacea, hemocyanins had long been considered unnecessary in the Myriapoda. Here we report the complete molecular structure of the hemocyanin from the common house centipede Scutigera coleoptrata (Myriapoda: Chilopoda), as deduced from 2D-gel electrophoresis, MALDI-TOF mass spectrometry, protein and cDNA sequencing, and homology modeling. This is the first myriapod hemocyanin to be fully sequenced, and allows the investigation of hemocyanin structure-function relationship and evolution. S. coleoptrata hemocyanin is a 6…
A multidomain xylanase from a Bacillus sp. with a region homologous to thermostabilizing domains of thermophilic enzymes
1999
The gene xynC encoding xylanase C from Bacillus sp. BP-23 was cloned and expressed in Escherichia coli. The nucleotide sequence of a 3538 bp DNA fragment containing xynC gene was determined, revealing an open reading frame of 3258 bp that encodes a protein of 120,567 Da. A comparison of the deduced amino acid sequence of xylanase C with known beta-glycanase sequences showed that the encoded enzyme is a modular protein containing three different domains. The central region of the enzyme is the catalytic domain, which shows high homology to family 10 xylanases. A domain homologous to family IX cellulose-binding domains is located in the C-terminal region of xylanase C, whilst the N-terminal r…
easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
2012
Video abstract A video abstract by the authors of this paper is available. video-abstract8870.mov
Ontology languages for the semantic web: A never completely updated review
2006
This paper gives a never completely account of approaches that have been used for the research community for representing knowledge. After underlining the importance of a layered approach and the use of standards, it starts with early efforts used for artificial intelligence researchers. Then recent approaches, aimed mainly at the semantic web, are described. Coding examples from the literature are presented in both sections. Finally, the semantic web ontology creation process, as we envision it, is introduced.
Photoswitchable Smectic Liquid-Crystalline Elastomers
2005
We succeeded in the synthesis of azo side chain containing polysioxanes with broad smectic C* and A phases. In these polymers the phase transition temperatures can be shifted reversibly by up to 17°C by irradiation with UV (cis) or VIS (trans) light. Thin films of these polymers in the smectie phase (both on substrates and as free-standing films) orient perfectly in a homeotropic manner. As a consequence, the aze chromophores do no longer absorb during a perpendicular illumination with light (dichroism). It is thus possible to crosslink these films photochemically to prepare photoswitchable smectic LC elastomers.
Human Brain Neuroglobin Structure Reveals a Distinct Mode of Controlling Oxygen Affinity
2003
Neuroglobin, mainly expressed in vertebrate brain and retina, is a recently identified member of the globin superfamily. Augmenting O(2) supply, neuroglobin promotes survival of neurons upon hypoxic injury, potentially limiting brain damage. In the absence of exogenous ligands, neuroglobin displays a hexacoordinated heme. O(2) and CO bind to the heme iron, displacing the endogenous HisE7 heme distal ligand. Hexacoordinated human neuroglobin displays a classical globin fold adapted to host the reversible bis-histidyl heme complex and an elongated protein matrix cavity, held to facilitate O(2) diffusion to the heme. The neuroglobin structure suggests that the classical globin fold is endowed …
Self-adjuvanting C18 lipid vinil sulfone-PP2A vaccine: study of the induced immunomodulation against Trichuris muris infection
2017
Despite the importance of the adjuvant in the immunization process, very few adjuvants merge with the antigens in vaccines. A synthetic self-adjuvant oleic-vinyl sulfone (OVS) linked to the catalytic region of recombinant serine/threonine phosphatase 2A from the nematode Angiostrongylus costaricensis (rPP2A) was used for intranasal immunization in mice previously infected with Trichuris muris . The animal intranasal immunization with rPP2A-OVS showed a reduction of 99.01% in the number of the nematode eggs and 97.90% in adult. The immunohistochemical analysis of the intestinal sections showed that in immunized animals with lipopeptide the mucus was significantly higher than in the other ex…
Lattice Boltzmann Simulations at Petascale on Multi-GPU Systems with Asynchronous Data Transfer and Strictly Enforced Memory Read Alignment
2015
The lattice Boltzmann method is a well-established numerical approach for complex fluid flow simulations. Recently general-purpose graphics processing units have become accessible as high-performance computing resources at large-scale. We report on implementing a lattice Boltzmann solver for multi-GPU systems that achieves 0.69 PFLOPS performance on 16384 GPUs. In addition to optimizing the data layout on the GPUs and eliminating the halo sites, we make use of the possibility to overlap data transfer between the host CPU and the device GPU with computing on the GPU. We simulate flow in porous media and measure both strong and weak scaling performance with the emphasis being on a large scale…
Optimal Control of Dissipative Quantum Systems
2008
We study the control of finite dimensional quantum systems by external laser fields. After examining the concrete example of the diatomic molecular alignment in dissipative media, we are interested in the problem of optimal control, where the objective is to bring the system from an initial state into a given final state while minimizing a cost functional. The Pontryagin maximum principle (PMP) provides necessary conditions for optimality, by establishing that any optimal trajectory is the extremal solution of an extended problem of Hamiltonian structure. In this context, we perform the analysis of two particular systems. The first one is a dissipative 2-level system, for which we determine…