Update China geodetic coordinate frame considering plate motion

China Geodetic Coordinate System 2000 (CGCS2000), as the formal national coordinate reference frame, has been used for 20 years. The coordinates of all Global Navigation Satellite System (GNSS) stations in China need referring to this system. To this end, the first step is to align the coordinates of all stations, usually included in a regional GNSS network, with a given International Terrestrial Reference Frame (ITRF), then these coordinates are corrected to the CGCS2000 in consideration of plate movement. For a better alignment result, regional control stations are needed and their coordinates were estimated from the combination of constraint-free normal equation systems provided by several International GNSS Service (IGS) analysis centers. The effect in using these refined coordinates, which determine a regional coordinate datum, on the alignment result should be evaluated by the coordinate corrections of the regional control stations to the regional coordinate datum, i.e. smaller corrections mean better alignments of the two associated frames. The test results show that the refined coordinates are more accurate than the ones calculated from the station's velocity, and are well aligned with the ITRF2005. Moreover, for obtaining the coordinates of GNSS stations in an updated CGCS2000 frame, a gridded linear velocity field based on the estimated velocities at 1025 CGCS2000 stations was generated for mainland China using the optimal interpolation method, the inverse distance weighting, which is selected from five interpolation methods. The overall precisions of the constructed velocity field at all stations in the East (E) and, North (N) directions are 0.78 mm/a and 0.95 mm/a, respectively. For evaluating the accuracy of the updated CGCS2000 frame, monthly solutions for the coordinates of some CGCS2000 CORS stations in the ITRF2014 during the period from 2000.0 to 2018 were obtained and the Root Mean Square (RMS) of the differences between the coordinates corrected to the CGCS2000 and the known coordinates at these stations are about 2–3 cm.

GSAlign – an efficient sequence alignment tool for intra-species genomes

Personal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation. Though many methods have been developed, some are designed for small genome comparison while some are not efficient for large genome comparison. Moreover, most existing genome comparison tools have not been evaluated the correctness of sequence alignments systematically. A wrong sequence alignment would produce false sequence variants. In this study, we present GSAlign that handles large genome sequence alignment efficiently and identifies sequence variants from the alignment result. GSAlign is an efficient sequence alignment tool for intra-species genomes. It identifies sequence variations from the sequence alignments. We estimate performance by measuring the correctness of predicted sequence variations. The experiment results demonstrated that GSAlign is not only faster than most existing state-of-the-art methods, but also identifies sequence variants with high accuracy.

locBLAST v2.0 - an improved PHP library for embedding standalone NCBI BLAST+ program to an interactive graphical user interface

BackgroundNCBI BLAST is a most popularly used sequence analysis platform in a broad range of applications. The final release of standalone WWW BLAST server (wwwBLAST v2.2.26) of NCBI was officially released on May 10, 2004, and discontinued its support. Due to the popularity and high demand, the BLAST algorithms were refined with rich features and released as online BLAST, standalone BLAST+, BLAST RESTful service, and cloud BLAST server. locBLAST v2.0 is a lightweight PHP library, designed in preference to WWW BLAST server. It masks command-line BLAST+ programs to a rich graphical user interface (GUI).MethodsThe locBLAST v2.0 library was designed using PHP, CSS, pure JavaScript, and standalone NCBI BLAST+ executables.ResultslocBLAST v2.0 provides an interactive web interface to input query sequences through the web form and provides a graphical report of the sequence alignment result. The graphical overview, tabular summary, and formatted sequence alignment of locBLAST v2.0 result mimic to the native format of online NCBI BLAST result. It allows users to perform both local and online database search.AvailabilityFreely available at https://github.com/AshokHub/locBLAST

Two-Level Parallel Alignment Based on Sequence Parallel Vectorization

This paper proposed a way of two-level parallel alignment based on sequence parallel vectorization with GPU acceleration on the Fermi architecture, which integrates sequence parallel vectorization, parallel k-means clustering approximate alignment and parallel Smith-Waterman algorithm. The method converts sequence alignment into vector alignment by first. Then it uses k-means alignment to divide sequences into several groups and reduce the size of sequence data. The expected accurate alignment result is achieved using parallel Smith-Waterman algorithm. The high-throughput mouse T-cell receptor (TCR) sequences were used to validate the proposed method. Under the same hardware condition, comparing to serial Smith-Waterman algorithm and CUDASW++2.0 algorithm, our method is the most efficient alignment algorithm with high alignment accuracy.

Genetic diversity and hybridization of Pulsatilla tongkangensis based on the nrDNA ITS region sequence

Pulsatilla tongkangensis, a perennial medicinal herb growing on the cliffs of Tongkang, Kangwon Province, Korea, is accordingly named as P. tongkangensis as a new Pulsatilla species. Due to sharing similar morphological characters with other Pulsatilla species, how to accurately discriminate P. tongkangensis becomes a critical, urgently needed-solved problem. To understand the truth of P. tongkangensis derivation and the phylogenetic relationship in Pulsatilla, the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) as the most frequently used marker for distinguishing plant species was amplified from P. tongkangensis in this study. According to sequence alignment result, three P. tongkangensis-specific nucleotide sites were obtained to vary from other Pulsatilla species, particularly one at 417 bp showing completely homology among P. tongkangensis accessions and completely dissimilarity between P. tongkangensis and other Pulsatilla species. As known fungal contamination is common in herbal medicinal materials when improperly processed and stored, using universal primers of the ITS region could not only plant DNA but parasitic fungal DNA. Thus, to improve the amplification condition of the ITS region from P. tongkangensis and design plant-specific primer would the following focus of our study. This work will be useful for clearly understanding the phylogenetic relationship between P. tongkangensis and other species belonging to the genus Pulsatilla.

Multiple Factors Integration Based Text Alignment for Medical Database

The analysis and processing of medical data is very valuable, and the alignment for medical database in sentence level plays an important role in which. Among the existing sentence alignment approaches, the error propagation problem highly impacts the precision of the alignment result. This paper proposed a multiple factors integration based sentence alignment model (MFI). The MFI model integrated multiple factors to acquire the similarity map for sentence aligning; and used optimization matching strategy to get the alignment between the bilingual text. Experiments showed that, due to the introduction of the MFI model, the error propagation was avoid or relieved. And the overall error rate of sentence alignment was reduced by 20%.

Improving Managerial Training Services in Project-Oriented Organizations with an Ontology-Alignment-Based Recommendation Mechanism

This chapter proposes a recommendation mechanism to enhance the managerial training in Project-Oriented Organizations (POOs). The mechanism is presented within the framework of an innovative system used to provide support to POOs during the acquisition and implementation of training services. The recommender engine has, as inputs, the knowledge gaps of the employees given by an assessment system and the alignment in RDF/XML format between two ontological representations: one for the management documents provided by POOs and one for the training curriculum offered to the POOs. The recommender engine makes suggestions for adapting the training curriculum to the POOs’ needs, by translating the ontology alignment result into a user-friendly form and by identifying Web resources suitable to fill up the knowledge gaps. The outputs are smart recommendations meant to personalize the training curriculum to POOs and, thus, to increase the competitiveness of POOs.

ON COMPARING TWO STRUCTURED RNA MULTIPLE ALIGNMENTS

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at . A jar file of the program is also available for download from the web server.