Conde Lucía, Vaquerizas Juan M, Santoyo Javier, Al-Shahrour Fátima, Ruiz-Llorente Sergio, Robledo Mercedes, Dopazo Joaquín
Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W242-8. doi: 10.1093/nar/gkh438.
We have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.
我们开发了一个网络工具——PupaSNP Finder（简称PupaSNP），用于高通量搜索具有潜在表型效应的单核苷酸多态性（SNP）。PupaSNP以基因列表作为输入（或根据染色体坐标生成基因列表），并检索可能影响细胞机制用于正确处理基因的保守区域（内含子/外显子边界或外显子剪接增强子）、预测的转录因子结合位点（TFBS）以及蛋白质中氨基酸变化的SNP。该程序使用Ensembl提供的基因组中SNP的映射。此外，用户定义的SNP（尚未在基因组中映射）可以轻松提供给该程序。此外，还提供了来自基因本体论、OMIM以及其他模式生物中的同源性的额外功能信息。与其他现有程序不同，其他程序仅关注可能对蛋白质有影响的SNP，而PupaSNP还包括可能具有转录效应的SNP。PupaSNP在多因素疾病研究中将有很大帮助，其中使用功能性SNP将提高识别导致疾病的基因的敏感性。可通过http://pupasnp.bioinfo.cnio.es访问PupaSNP网络界面。
