Search results for " alignment"
showing 10 items of 587 documents
Parallel and scalable short-read alignment on multi-core clusters using UPC++
2016
[Abstract]: The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the …
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…
Identification and functional expression of HCx31.9, a novel gap junction gene
2002
By combining in silico and bench molecular biology methods we have identified a novel human gap junction gene that encodes a protein designated HCx31.9. We have determined its human chromosomal location and gene structure, and we have identified a putative mouse ortholog, mCx30.2. We have observed the presence of HCx31.9 in human cerebral cortex, liver, heart, spleen, lung, and kidney and the presence of mCx30.2 in mouse cerebral cortex, liver and lung. Moreover, preliminary data on the electrophysiological properties of HCx31.9 have been obtained by functional expression in paired Xenopus oocytes and in transfected N2A cells.
Tibial tubercle osteotomy: effect of different osteotomy planes on contact surface area and tubercle anteriorization
2022
In 1983, Fulkerson introduced a technique of tibial tubercle osteotomy performed according to an inclined plane with respect to frontal plane. Due to obliquity of the osteotomy plane, this procedure allows both anterior and medial transfer of the tibial tubercle. The purpose of the study was to investigate the influence of the different degrees of the oblique plane of osteotomy on anterior displacement and the contact surface area of tibial tubercle. Synthetic bones were used for the study. An osteotomy of the tibial tubercle (TT) was performed in each specimen. Specifically, 3 different degrees of osteotomy planes relative to the reference frontal plane were examined: 20°, 30° and 40°. On …
Primary structure and unusual carbohydrate moiety of functional unit 2-c of keyhole limpet hemocyanin (KLH)
1999
Abstract The complete amino acid sequence of the Megathura crenulata hemocyanin functional unit KLH2-c was determined by direct sequencing and matrix-assisted laser desorption ionization mass spectrometry of the protein, and of peptides obtained by cleavage with EndoLysC proteinase, chymotrypsin and cyanogen bromide. This is the first complete primary structure of a functional unit c from a gastropod hemocyanin. KLH2-c consists of 420 amino acid residues. Circular dichroism spectra indicated approx. 31% β-sheet and 29% α-helix contents. A multiple sequence alignment with other molluscan hemocyanin functional units revealed average identities between 41 and 49%, but 55% in case of Octopus he…
Orientation and Dynamics of ZnO Nanorod Liquid Crystals in Electric Fields.
2010
ZnO nanorod polymer hybrids (i.e., ZnO nanorods coated with a block copolymer with a short anchor block (dopamine) and a longer solubilizing block of polystyrene (PS)) form liquid crystalline (LC) phases if they are dispersed at high concentration e.g., in a PS oligomer matrix. Due to the high mobility of the low T(g)-matrix the nanorod polymer hybrids show a switching behavior under an applied AC electric field. Hence, the orientation of the nanorod mesogens can be changed from planar (parallel to the substrate) to homeotropic (perpendicular) in full analogy to the switching of low molecular liquid crystals in an electric field. Dielectric measurements show that such a switching is mainly …
Assessing divergence time of Spirulida and Sepiida (Cephalopoda) based on hemocyanin sequences
2011
Abstract The phylogenetic position of the mesopelagic decabrachian cephalopod Spirula is still a matter of debate. Since hemocyanin has successfully been used to calibrate a molecular clock for many molluscan species, a molecular clock was calculated based on this gene with special attention to the cephalopod genera Spirula and Sepia. The obtained partial sequence comprising ca., one third (3567 bp) of the complete gene is similar to that of Sepia officinalis. The molecular clock was calibrated using the splits of Gastropoda–Cephalopoda (ca. 550 ± 50 mya) and Heterobranchia–Vetigastropoda (ca. 380 ± 10 mya). The resulting hemocyanin-based molecular clock is stable, and the estimated diverge…
Nanosecond-level time synchronization of autonomous radio detector stations for extensive air showers
2016
To exploit the full potential of radio measurements of cosmic-ray air showers at MHz frequencies, a detector timing synchronization within 1 ns is needed. Large distributed radio detector arrays such as the Auger Engineering Radio Array (AERA) rely on timing via the Global Positioning System (GPS) for the synchronization of individual detector station clocks. Unfortunately, GPS timing is expected to have an accuracy no better than about 5 ns. In practice, in particular in AERA, the GPS clocks exhibit drifts on the order of tens of ns. We developed a technique to correct for the GPS drifts, and an independent method is used to cross-check that indeed we reach a nanosecond-scale timing accura…
Absolute momentum calibration of the HARP TPC
2008
In the HARP experiment the large-angle spectrometer is using a cylindrical TPC as main tracking and particle identification detector. The momentum scale of reconstructed tracks in the TPC is the most important systematic error for the majority of kinematic bins used for the HARP measurements of the double-differential production cross-section of charged pions in proton interactions on nuclear targets at large angle. The HARP TPC operated with a number of hardware shortfalls and operational mistakes. Thus it was important to control and characterize its momentum calibration. While it was not possible to enter a direct particle beam into the sensitive volume of the TPC to calibrate the detect…
Alignment of the ALICE Inner Tracking System with cosmic-ray tracks
2010
ALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 micron in some cases (pixels). The sources of alignment information include survey measurement…