生物资讯及网路资源简介

1、生物資訊及網路資源簡介蔡少正國立成功大學醫學院生理所國立成功大學生物資訊中心定義：利用電腦輔助資料管理系統從基因體(Genomic)、蛋白質體(proteomics)或藥物篩選資料庫中蒐集、整合、及分析大量的生物序列或資訊。基因資料庫（Genbank)序列資訊快速增加生物資訊學的發展# bp in billions1231982-2000生物資訊學(Bioinformatics)與人類基因組解讀計劃(Human Genome Project)序列資料貯存- (6 * 106序列檔案/one genome) * 6 * 200 KB/序列檔案序列資訊整理- BLAST, FASTA. 序列資訊分

2、析- Assembly, repetitive sequence. 序列功能註解 - Genome annotation, molecular modeling生物資訊學的發展涵蓋分子生物、資訊工程、統計等學門的新科學計算生物學(computational biology)：處理生物(序列)資料的科學蘊涵無限寶藏的科學-序列取得、結構分析、功能預測、模擬驗證。生物資訊學的發展後基因體分析紀元(Post-genome Era)功能性基因體(Functional Genomics) 世代來臨當基因被完全解讀出來後下一階段的目標：組合一個沒有“間隙” (Gap)的染色體圖譜，並且提高序列正確率至99

3、.99%-基因註解-基因預測-蛋白質功能研究(proteomics)-單核甘酸多樣性(single nucleotide polymorphisms or SNPs)功能性基因體(Functional Genomics)辨認所有的基因並瞭解他們的功能：Different technologies and resources into a proteomic process LITERATURE （文獻）DATABASES NUCLEOTIDE （核酸）DATABASES PROTEIN （蛋白質）DATABASES ENZYME （酵素）DATABASES OTHER TYPE （其他）DAT

4、ABASES資料庫的類型：依性質區分資料庫的類型：依功能區分原始資料庫Genebank, ESTdatabase加值型資料庫初步或未加整理的序列資訊比對、計算、整理只擷取部分有用的資訊加以歸類儲存重複序列資料庫、訊息傳遞因子資料庫(Smart database)實用價值較低具高附加價值/dbEST/index.htmlSMART - Simple Modular Architecture Research Tool NCBI網路資源 vs. 套裝軟體網路資源的優缺點 優點:- 資料庫更新頻繁- 介面較易學習，操作容易 缺點:- 通常功能專一化- 資料格式轉換不易- 參數預設值無法調整- 解讀輸

5、出結果困難網路資源 vs. 套裝軟體套裝軟體的優缺點 優點:- 容易調整參數預設值- 分析功能完整且具多樣化- 資料格式統一，不同程式間不需轉換- 可提供圖形檔輸出結果 缺點:- 資料庫更新較不頻繁- 指令繁多不易學習網際網路上的生物資源Search EngineBioHunt /BioHunt/Infomine /Pedros Biomolecular Research Tools /pedro/research_tools.html網際網路上的生物資源DatabasesLiterature-PubMed, Hint, SeqAnalRef, SRSSequence -DNA: GenBan

6、k/ EMBL/ DDBJ, UniGene, GDB-Protein: PDB, PIR, PROSITE, SWISS-PORTStructure- BioMagResBank, SCOP, MMDB網際網路上的生物資源Software (DNA annotation)Nucleic Acid Conformation- DNA, RNA secondary structureTranslation- start and stop coden, coden usage tableORF Finder- promoter, 5and 3 UTR, intron and exon Gene F

7、unction Prediction- motif and pattern search 網際網路上的生物資源Software (Protein annotation) Identification and characterization DNA - Protein Similarity searches Pattern and profile searches Post-translational modification prediction Primary structure analysis Secondary structure prediction Tertiary struct

8、ure Transmembrane regions detection Alignment 網際網路上的生物資源Courses陽明大學生化所 清華大學生科系 中研院生圖 國家衛生研究院生物資訊課程 國立成功大學醫學院Bioinformatics Package ToolsGCG - The Wisconsin Package Accelrys Biocomputational ResearchGenoMax v3.3 InforMaxLSITM Lion BioscienceBioinformatics Package ToolsLaserGene - DNAStar, Inc.MacVect

9、or - Oxford Molecular Group, Inc.Discovery Studio Gene - Oxford Molecular Group, Inc.Vector NTI - Informax, Inc.Literature, Bibliography and Reference DatabasesMedlineMIM(Mendelian Inheritance in Man)TaxonomyGeneticodeMIM(Mendelian Inheritance in Man)Browsing OMIM Nucleotide sequence databasesEMBL/G

10、enebank/DDBJContaining every individually submitted primary sequenceREFSEQProvide non-redundant curated data representing knowledge of Known genes ENSEMBLannotated genomic contig sequenceThe International Nucleotide Sequence Database Collaboration (INSD) The INSD consists of DDBJ (Japan), GenBank (U

11、SA) and the EMBL (UK) Nucleotide Sequence Database. The three databases exhange new and updated data on a daily basis to achieve optimal synchronisationGenebankProtein sequence databasesSwiss-Prota curated protein sequence database which strives to provide a high level of annotation. SpTrEMBLa datab

12、ase supplementing the Swiss-Prot Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) EMBLPIRidentification and analysis of protein sequences and their corresponding coding sequences REFSEQPProtein information from REFSEQSPTrEMBLPrimary sequence could be further

13、 analysisSequence database with analyzed annotation(special pattern found) Analysis toolsNucleotide related databasesSpecial pattern of Nucleotide sequenceREBASE Genome structureCPGISLAND, ENSEMBLCPG, LOCUSLINK, MOUSE2HUMANTranscription factor binding siteTESS: TFCLASS, TFCELL, TFFACTOR, TFMATRIX, TFSITE Gene structureEPD, TFGENE, UTR, UTRSITE, EMBLALIGN integration of gene expression patternUNIGENE UNILIB Locuslink PDB二維電泳資料庫2D Gel預測人類的基因利用其他物種的基因利用某一染色體上的基因數利用EST資料庫中的序列傳統的方法Pfam http:/www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF02024http:/www.b