• Genomics & Informatics
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• v.8 no.2
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• pp.97-99
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• 2010

To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In this respect, a format conversion tool, as well as quality conversion tool would be the minimum requirements to integrate reads from different platforms. We have developed the Pyrus NGS Sequencing Format Converter, a simple software toolkit which allows to convert three kinds of Next Generation Sequencing reads, into commonly used fasta or fastq formats. The converter modules are all implemented, uniformly, in Java GUI modules that can be integrated in software applications for displaying the data content in the same format.

• Journal of Ginseng Research
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• v.41 no.3
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• pp.339-346
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• 2017

Background: In this study, we investigated how to convert the Panax ginseng DNA sequence code and chemical fingerprints into a two-dimensional code. In order to improve the compression efficiency, GATC2Bytes and digital merger compression algorithms are proposed. Methods: HPLC chemical fingerprint data of 10 groups of P. ginseng from Northeast China and the internal transcribed spacer 2 (ITS2) sequence code as the DNA sequence code were ready for conversion. In order to convert such data into a two-dimensional code, the following six steps were performed: First, the chemical fingerprint characteristic data sets were obtained through the inflection filtering algorithm. Second, precompression processing of such data sets is undertaken. Third, precompression processing was undertaken with the P. ginseng DNA (ITS2) sequence codes. Fourth, the precompressed chemical fingerprint data and the DNA (ITS2) sequence code were combined in accordance with the set data format. Such combined data can be compressed by Zlib, an open source data compression algorithm. Finally, the compressed data generated a two-dimensional code called a quick response code (QR code). Results: Through the abovementioned converting process, it can be found that the number of bytes needed for storing P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can be greatly reduced. After GTCA2Bytes algorithm processing, the ITS2 compression rate reaches 75% and the chemical fingerprint compression rate exceeds 99.65% via filtration and digital merger compression algorithm processing. Therefore, the overall compression ratio even exceeds 99.36%. The capacity of the formed QR code is around 0.5k, which can easily and successfully be read and identified by any smartphone. Conclusion: P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can form a QR code after data processing, and therefore the QR code can be a perfect carrier of the authenticity and quality of P. ginseng information. This study provides a theoretical basis for the development of a quality traceability system of traditional Chinese medicine based on a two-dimensional code.

• Journal of Internet Computing and Services
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• v.5 no.5
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• pp.1-15
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• 2004

In this paper, we explain the design and implementation of GWB(Gene WorkBench), which is a web-based, integrated system for efficiently managing and analyzing genomic sequences, Most existing software systems handling genomic sequences rarely provide both managing facilities and analyzing facilities. The analysis programs also tend to be unit programs that include just single or some part of the required functions. Moreover, these programs are widely distributed over Internet and require different execution environments. As lots of manual and conversion works are required for using these programs together, many life science researchers suffer great inconveniences. in order to overcome the problems of existing systems and provide a more convenient one for helping genomic researches in effective ways, this paper integrates both managing facilities and analyzing facilities into a single system called GWB. Most important issues regarding the design of GWB are how to integrate many different analysis programs into a single software system, and how to provide data or databases of different formats required to run these programs. In order to address these issues, GWB integrates different analysis programs byusing common input/output interfaces called wrappers, suggests a common format of genomic sequence data, organizes local databases consisting of a relational database and an indexed sequential file, and provides facilities for converting data among several well-known different formats and exporting local databases into XML files.