Gagniuc P, Cimponeriu D, Ionescu-Tîrgovişte C, Mihai Andrada, Stavarachi Monica, Mihai T, Gavrilă L
Department of Genetics, University of Bucharest, Romania. paulgagniuc@yahoo
Rom J Intern Med. 2011;49(2):121-8.
In order to make a step forward in the knowledge of the mechanism operating in complex polygenic disorders such as diabetes and obesity, this paper proposes a new algorithm (PRSD -possible restriction site detection) and its implementation in Applied Genetics software. This software can be used for in silico detection of potential (hidden) recognition sites for endonucleases and for nucleotide repeats identification. The recognition sites for endonucleases may result from hidden sequences through deletion or insertion of a specific number of nucleotides. Tests were conducted on DNA sequences downloaded from NCBI servers using specific recognition sites for common type II restriction enzymes introduced in the software database (n = 126). Each possible recognition site indicated by the PRSD algorithm implemented in Applied Genetics was checked and confirmed by NEBcutter V2.0 and Webcutter 2.0 software. In the sequence NG_008724.1 (which includes 63632 nucleotides) we found a high number of potential restriction sites for ECO R1 that may be produced by deletion (n = 43 sites) or insertion (n = 591 sites) of one nucleotide. The second module of Applied Genetics has been designed to find simple repeats sizes with a real future in understanding the role of SNPs (Single Nucleotide Polymorphisms) in the pathogenesis of the complex metabolic disorders. We have tested the presence of simple repetitive sequences in five DNA sequence. The software indicated exact position of each repeats detected in the tested sequences. Future development of Applied Genetics can provide an alternative for powerful tools used to search for restriction sites or repetitive sequences or to improve genotyping methods.
为了在了解糖尿病和肥胖症等复杂多基因疾病的发病机制方面取得进展，本文提出了一种新算法（PRSD - 可能的限制位点检测）及其在应用遗传学软件中的实现。该软件可用于在计算机上检测核酸内切酶的潜在（隐藏）识别位点以及识别核苷酸重复序列。核酸内切酶的识别位点可能是由于特定数量核苷酸的缺失或插入而产生的隐藏序列导致的。使用软件数据库中引入的常见II型限制酶的特定识别位点，对从NCBI服务器下载的DNA序列进行了测试（n = 126）。应用遗传学中实现的PRSD算法指示的每个可能的识别位点都通过NEBcutter V2.0和Webcutter 2.0软件进行了检查和确认。在序列NG_008724.1（包含63632个核苷酸）中，我们发现了大量可能由一个核苷酸的缺失（n = 43个位点）或插入（n = 591个位点）产生的ECO R1潜在限制位点。应用遗传学的第二个模块旨在找到简单重复序列的大小，这对于理解单核苷酸多态性（SNP）在复杂代谢疾病发病机制中的作用具有实际意义。我们已经测试了五个DNA序列中简单重复序列的存在情况。该软件指出了在测试序列中检测到的每个重复序列的确切位置。应用遗传学的未来发展可以为用于搜索限制位点或重复序列或改进基因分型方法的强大工具提供一种替代方案。
