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1、BioNumerics生物信息分析统一平台生物信息分析统一平台上海一贝科技 许先生 15821483715One powerful platform for databasing, analyzing, and sharing all your biological data BioNumericsBioNumericsBioNumerics7.1模块Data modules 数据模块数据模块Fingerprint Data. Normalization and analysis of electrophoresis fingerprints from slab gels, automated
2、 sequencers, and lab-on-a chip systems. Preprocessing and analysis of spectral data such as MALDI.Character Data. Import and analyze character data from a wide range of sources including phenotype panels, antibiotic resistance profiles, microarrays, etc.Sequence Data. Assemble and analyze Sanger seq
3、uence data and NGS sequence reads. Access a wide variety of sequence analysis, search and alignment, and comparison tools.Whole Genome Map Data. Align and cluster whole genome maps for bacterial strain typing and identification.Trend Data. Analyze sequential measurements that express an evolution of
4、 one parameter in function of another, e.g., enzymatic activity, growth curves, rt-PCR, etc.Analysis modulesTree and Network Inference. Select from an impressive range of clustering algorithms to calculate evolutionary trees and relationship networks. Display confidence levels on clusters and branch
5、es.Dimensioning and Matrix Mining. Create non-hierarchical groupings using various ordination techniques such as principal components analysis, multidimensional scaling, discriminant analysis, and identify discriminating features between groups. Perform in-depth analysis of character matrices.Genome
6、 Analysis Tools. Align and compare chromosomes side-by-side or calculate multiple chromosome alignments. Calculate SNPs and mutations on multi-chromosome alignments and annotate new chromosomes. Perform microbial metagenomics diversity analysis.Classifiers and Identification. Identify unknown sample
7、s against reference data sets using state-of-the-art classifiers such as Naive Bayesian, SVM, Shrunken Centroids, and a range of similarity coefficients. Enhance your identification projects with parameter optimization and comprehensive cross-validation tools. Compare and validate different techniqu
8、es or procedures.Versioning and Audit Trails. Create audited databases (fully FDA Title 21 CFR Part 11 compliant) by recording all changes and keeping all versions of selected database objects. Compare and restore versions. Log user activity, create digital signing privileges.我们能存储什么？OrgnismField1:
9、GenusField2: pecies信息字段信息字段字符数据字符数据AGCTCAAGCTGA序序 列列l定义多达80个信息字段l链接外部数据库ll表型特征l抗菌敏感特征l生化和形态特征l微阵列（基因芯片）ll凝胶图像lSequencer 图谱（e.g. AFLP）llDNA & 核酸序列（e.g. 16S rRNA）l指指纹图谱纹图谱我们能做什么？查查 询询OrgnismField1: GenusField2: pecies亲缘亲缘分析分析Using fieldsUsing experimentsUsing ranges of valuesUsing any combinationsMult
10、iple alignmentNeighbor JoiningParsimonyMaximun likelihoodMANOVA(多元方差分析)Discriminant annlysisK-means,JacknifeSignificance testingPricipal Components AnalysisMulti-Dim. ScalingSelf-Organizing MapsNeural NetworksUPGMA,NN,FN,WardStandard deviationCophenetic correlationBootstrapLibrary construtionStatist
11、ical confidenceNeural Networks数理数理统计统计聚聚类类分析分析鉴鉴 定定DATABASE多多维维分析分析Bionumerics在疾控系统的主要应用在疾控系统的主要应用MLST(多位点序列分析多位点序列分析) 实验和分析方法已经标准化，有国际数据库供查询和比对 成功应用于全球、全国性暴发调查和菌型分布调查 适合用于长期的、大范围的流行病学调查和监测菌群结构变化PFGE(脉冲场电泳脉冲场电泳) 被广泛承认和使用的方法 分辨能力优于MLST，分型结果与MLST有很高的一致性 可以作为MLST实验菌株的初筛工具 可以为暴发和聚集性病例调查提供实验室数据支持MLVA (多位
12、点可变数目串联重复序列分型多位点可变数目串联重复序列分型) 在肠道菌和食源性疾病的暴发调查中已经被证实具有作用 在呼吸道细菌中分型结果类似于MLST，分辨力高于PFGE和MLST 需要寻找稳定的VNTR位点组合用于流行病学调查和菌群结构分析2003-2008年371株脑膜炎奈瑟菌MLST分析应用实例一：脑膜炎奈瑟菌种群结构分析和流行分布ST-4821型ST-4821型ST-7型ST-7型2003-2008年脑膜炎奈瑟菌主要序列群分布暴发相关菌株健康携带本底菌株健康携带本底菌株应用实例二：流脑暴发调查流脑菌株总携带率：28.3暴发相关菌株携带率：15.7%应用实例三：肺炎克雷伯菌院内感染鉴别应用
13、实例四：热带念珠菌种群结构分析Cluster ICluster II猪链球菌猪链球菌血清二型血清二型种群关系种群关系应用实例五：热带念珠菌种群结构分析应用实例六：MLVA数据MST分析发现Cluster分型数据提交聚类分析“Visual Check”完全一致的分子分型特征应用实例七：发现各种Cluster应用实例八：分子流病应用Pattern趋势长期监测:观察pattern的变化趋势是否一如既往的稳定Pattern频率长期监测:观察pattern出现频率是否有较大变化应用实例九：归因分析归因分析引起食源性疾病的各种食品所占的比例（相对贡献）。Distance and similarity matricesCustomized display of test panelsCharacter import from a text file or an Excel spreadsheet一代、二代测序应用一代、二代测序应用RT-PCR/RT-PCR/趋势类数据分析趋势类数据分析序列比对、序列拼接、同源性分析、酶切位点查找、引物设计、蛋白分析序列分析序列分析全基因组数据分析全基因组数据分析物种分类和鉴定物种分类和鉴定绘制图谱绘制图谱数据数据建库建库及共享及共享Thanks for your Attention
