MiRE: a graphical R package for microRNA-related analysis / 中国医学科学杂志(英文版)

<p><b>OBJECTIVE</b>To provide a set of useful analysis tools for the researchers to explore the microRNA data.</p><p><b>METHODS</b>The R language was used for generating the Graphical Users Interface and implementing most functions. Some Practical Extraction and Report Language (Perl) scripts were used for parsing source files.</p><p><b>RESULTS</b>We developed a graphical R package named miRE, which was designated for the analysis of microRNA functions, genomic organization, etc. This package provided effective and convenient tools for molecular biologists to deal with routine analyses in microRNA-related research. With its help, the users would be able to build a desktop-centered microRNA research environment quite easily and effectively. miRE is freely available at http://www. biosino.org/-kanghu/WorkPresentation/miRE/miRE.html. A detailed user manual and tutorials with example code and image are also available.</p><p><b>CONCLUSION</b>miRE is a tool providing an open-source, user-friendly, integrated interface for microRNA-related analysis. With its help, researchers can perform microRNA-related analysis more efficiently.</p>

Bioinformatic identification and analysis of Schistosoma japonicum adenine phosphoribosyltransferase / 南方医科大学学报

<p><b>OBJECTIVE</b>To identify adenine phosphoribosyltransferases in Schistosoma japonicum and analyze their structural features.</p><p><b>METHODS</b>Based on the accessible transcriptome and proteomic data, the S. japonicum adenine phosphoribosyl transferases were identified using bioinformatics approaches including bi-directional homology comparison, domain search and phylogenetic analysis. Homology modeling was also performed to describe the structural features of the proteins.</p><p><b>RESULTS AND CONCLUSION</b>Two homologue sequences of adenine phosphoribosyltransferase were obtained from S. japonicum, and the EST abundance, physico-chemical properties and three-dimensional structures of them were also acquired.</p>

GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm / 中国医学科学院学报

<p><b>OBJECTIVE</b>To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery.</p><p><b>METHODS</b>Gpat, which is based on SPLASH algorithm, was developed by using open source software.</p><p><b>RESULTS</b>GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license.</p><p><b>CONCLUSION</b>Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.</p>