NHGRI/DIR Bioinformatics and Scientific Programming Core

NHGRI生物信息学和科学编程核心通过提供生物信息学和计算分析方面的专业知识和帮助，积极支持NHGRI研究人员正在进行的研究。核心促进获得专业的软件和硬件，开发通用的软件解决方案，可以解决基因组研究中的各种问题，开发数据库解决方案，用于有效存档和检索实验和临床数据，向基因组社区传播新的软件和数据库解决方案。并为NHGRI研究人员和受训人员提供生物信息学方面的教育机会。 在2008-2009年完成的科学项目包括设计同源结构域资源网站，分析人类和鸡基因的3个非翻译区之间的序列保守性，鉴定ATAD 5的推定直系同源物并产生多序列比对，将数十万个斑马鱼耳特异性MPSS标签映射到各种斑马鱼序列数据库，重新注释定制的斑马鱼寡核苷酸阵列，鉴定超过70个基因组区域的人类和三种灵长类动物之间的固定差异，并将祖先和衍生状态分配给来自相同区域的SNP;分析易位断裂点，提取700个小鼠基因的上游序列及其来自鸡、人和斑马鱼的直系同源物;更新和发布原位基因的网站<I></I>表达图像数据库，用RefSeqs、基因组坐标和SNP对来自GEO的微阵列平台进行注释;鉴定和分析含有MMP 8基因表达数据的GEO数据集，以及对恒河猴中SIV逆转录病毒整合位点的长期随访。 正在进行的科学项目包括重新设计组蛋白序列数据库，分析序列痕迹以检测肿瘤样本中假定致癌基因的突变，开发基于网络的产前调查，将传统的基于纸张的调查技术适应于基于网络的部署，开发血液学重要突变的网站和数据库，脊椎动物，无脊椎动物和植物基因组中大外显子的表征，乳腺癌信息核心（BIC）的持续更新和改进，使用Illumina序列标签绘制斑马鱼逆转录病毒整合位点的方法的开发，选择斑马鱼基因中基因调控区的预测，从CFTR UTR到人类基因组的22聚体的绘制，允许错配，开发用于管理癌症风险感知研究的基于Web的系统，分析调查报告和网络行为数据，开发定制的SQL数据库，用于存储和计算犬基因型、表型、序列、变异、样本数据和谱系数据的大量记录;开发各种Perl脚本，用于数据重新格式化，Magoh基因的进化分析，250，000个外显子列表中存在的SNP的鉴定，开发色素细胞基因的信息网站，在一组保守和非保守的非编码元件中注释在选定条件下起作用的转录因子的推定结合位点，整理多中心调查数据以研究葡萄糖脑苷脂酶突变和帕金森症之间的关联，汇编所有人RefSeq基因的基因组坐标的非冗余列表，比较MLV和CATPAC逆转录病毒载体的整合概况，并分析斑马鱼TILLING项目的序列痕迹以检测突变。

The NHGRI Bioinformatics and Scientific Programming Core actively supports the research being performed by NHGRI investigators by providing expertise and assistance in bioinformatics and computational analysis. The Core facilitates access to specialized software and hardware, develops generalized software solutions that can address a variety of questions in genomic research, develops database solutions for the efficient archiving and retrieval of experimental and clinical data, disseminates new software and database solutions to the genome community at-large, collaborates with NHGRI researchers on computationally-intensive projects, and provides educational opportunities in bioinformatics to NHGRI Investigators and trainees. Scientific projects completed in 2008-2009 include the design of the Homeodomain Resources Web site, analysis of sequence conservation between the 3 UTRs of orthologous human and chicken genes, identification of putative orthologs of ATAD5 and generation of a multiple sequence alignment, mapping of hundreds of thousands of zebrafish ear-specific MPSS tags to various zebrafish sequence databases, re-annotation of custom zebrafish oligonucleotide arrays, identification of fixed differences between human and three primates over 70 genomic regions, and assignment of the ancestral and derived state to SNPs from the same regions; analysis of a translocation breakpoint, extraction of upstream sequence for 700 mouse genes and their orthologs from chicken, human, and zebrafish; the update and release of a Web site for an <I>in situ</I> gene expression image database, annotation of a microarray platform from GEO with RefSeqs, genomic coordinates, and SNPs; identification and analysis of GEO datasets containing MMP8 gene expression data, and long-term follow-up on SIV retroviral integration sites in the rhesus macaque. Ongoing scientific projects include a redesign of the Histone Sequence Database, analysis of sequence traces to detect mutations in putative oncogenes in tumor samples, development of a Web-based prenatal survey, adaptation of traditional paper-based survey techniques for Web-based deployment, development of a Web site and database of hematologically important mutations, characterization of large exons in vertebrate, invertebrate, and plant genomes, ongoing updates and improvements to the Breast Cancer Information Core (BIC), development of a method to map zebrafish retroviral integration sites using Illumina sequence tags, prediction of gene regulatory regions in select zebrafish genes, mapping of 22-mers from the CFTR UTRs to the human genome, allowing for mismatches, development of a Web-based system for administering a cancer risk perception study, analysis of survey reports and Web behavior data, development of a customized SQL database for storing and computing on large numbers of records for canine genotypes, phenotypes, sequences, variations, sample data and pedigree data; development of various Perl scripts for data re-formatting, evolutionary analysis of the Magoh gene, identification of SNPs present in a list of 250,000 exons, development of an informational Web site for pigment cell genes, annotation of putative binding sites in a set of conserved and non-conserved non-coding elements for transcription factors that function in selected conditions, collation of multi-center survey data to study association between glucocerebrosidase mutations and Parkinsonism, compilation of a non-redundant list of the genomic coordinates of all human RefSeq genes, comparison of the integration profiles of the MLV and CATPAC retroviral vectors, and analysis of sequence traces to detection mutations for the zebrafish TILLING project.