SNP-RFLPing: restriction enzyme mining for SNPs in genomes
SNP-RFLPing: restriction enzyme mining for SNPs in genomes
复制标题
DOI：
10.1186/1471-2164-7-30
复制
发表时间：
2006-02-17
期刊：
影响因子：
4.4
通讯作者：
Chuang, LY
中科院分区：
文献类型：
--
作者：
Chang, HW;Yang, CH;Chuang, LY
背景资料：限制性片段长度多态性（RFLP）是单核苷酸多态性（SNP）基因分型的常用实验室方法。在这里，我们描述了一个基于网络的软件，命名为SNP-RFLPing，它提供了限制性内切酶的RFLP分析上的一批SNP和基因从人类，大鼠和小鼠genomes.Results：三个用户友好的输入包括：1）NCBI dbSNP的“rs”或“ss”ID; 2）NCBI的基因ID和HUGO基因名称; 3）任何格式的SNP-in-sequence，允许进行SNP-RFLPing分析。这些输入被自动编程为含SNP的序列及其互补序列，用于选择限制性内切酶。即使存在许多SNP，也提供每个输入基因的具有可用RFLP限制酶的所有SNP。SNP-RFLPing分析提供了cSNPs的SNP重叠群位置、杂合性、功能、蛋白残基和氨基酸位置，以及商业和非商业限制性内切酶。结论：该软件解决了同类软件的输入格式问题，大大简化了提供RFLP酶的程序。输入数据的混合自由形式对于执行SNP-RFLPing测定的用户是友好的。SNP-RFLPing为个性化医学的关联研究提供了一个节省时间的应用程序，可在http://bio.kuas.edu.tw/ snprflp/上免费获得。
Background: The restriction fragment length polymorphism ( RFLP) is a common laboratory method for the genotyping of single nucleotide polymorphisms ( SNPs). Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes.Results: Three user-friendly inputs are included: 1) NCBI dbSNP "rs" or "ss" IDs; 2) NCBI Entrez gene ID and HUGO gene name; 3) any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes.Conclusion: This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at http://bio.kuas.edu.tw/ snprflp/.