教你使用NCBI,PDB數(shù)據(jù)庫 ppt課件

1、Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochow第三講：序列的采集、存儲(chǔ)第三講：序列的采集、存儲(chǔ)和查詢和查詢 Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1,

2、Soochowr 1. DNA測序測序r 2. 序列數(shù)據(jù)的存儲(chǔ)序列數(shù)據(jù)的存儲(chǔ)r 3. 序列數(shù)據(jù)的文件格式序列數(shù)據(jù)的文件格式r 4. 序列數(shù)據(jù)的查詢序列數(shù)據(jù)的查詢Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. DNA一次測序的長度為一次測序的長度為500bp。r 2.基因組的測序方案：將大的染色體打斷成基因組的測序方案：將大的染色體打斷成100kbp的片斷，的片斷，插入到插入到BAC (Bacterial Artificial Chromosome)中

3、。再隨機(jī)打中。再隨機(jī)打斷，克隆，然后再組裝成長的序列斷，克隆，然后再組裝成長的序列(contig)。r 3. EST (Expressed sequence tag) 測序：細(xì)胞中測序：細(xì)胞中mRNA反轉(zhuǎn)錄反轉(zhuǎn)錄成成cDNA，方向不定，測序。，方向不定，測序。r 4. UniGene: 為每一個(gè)基因創(chuàng)造一個(gè)唯一的條目，收集這個(gè)為每一個(gè)基因創(chuàng)造一個(gè)唯一的條目，收集這個(gè)基因所有的基因所有的ESTs.r 5. GSS (基因組測序序列基因組測序序列)：類似于：類似于ESTs，來源基因組。，來源基因組。r 6. HTG (高通量基因組序列高通量基因組序列)：高通量、尚未完工的：高通量、尚未完工的DNA

4、序列。序列。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. DNA片段在染色體上的位置、方向已知。片段在染色體上的位置、方向已知。首先染色體被打斷成首先染色體被打斷成150kbp左右的片段，左右的片段，然后克隆到然后克隆到BACs中，再進(jìn)一步打碎，克隆，中，再進(jìn)一步打碎，克隆，測序，組裝。測序，組裝。r 2. “鳥槍法鳥槍法”，shotgun，隨機(jī)將，隨機(jī)將DNA片段打片段打碎，克隆，測序，組裝。碎，克隆，測序，組裝。DNA片段在染色片段在染色體上的

5、位置和方向未知。體上的位置和方向未知。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. 核酸三大數(shù)據(jù)庫：核酸三大數(shù)據(jù)庫：GenBank, EBI, DDBJ.r 2. Ensembl數(shù)據(jù)庫：基因組注釋。數(shù)據(jù)庫：基因組注釋。r 3. ESTs數(shù)據(jù)庫；數(shù)據(jù)庫；r 4. Uni

6、Gene數(shù)據(jù)庫數(shù)據(jù)庫r 5. Refseq數(shù)據(jù)庫；數(shù)據(jù)庫；r 6. NCBI的的Gene信息數(shù)據(jù)庫信息數(shù)據(jù)庫;r 7. 蛋白質(zhì)序列：蛋白質(zhì)序列：Swissprot/TrEMBL/UniProt數(shù)據(jù)庫。數(shù)據(jù)庫。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr161.0版，2019

7、.08Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochow2019.08，總序列，總序列45,660,524條，最多的條，最多的20個(gè)物種如下個(gè)物種如下Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009

8、-2010, Semester 1, Soochowr 1. 提供高質(zhì)量的，無冗余的，完整的序列提供高質(zhì)量的，無冗余的，完整的序列信息；信息；r 2. 包括基因組的包括基因組的DNA,轉(zhuǎn)錄成的轉(zhuǎn)錄成的RNA以及蛋以及蛋白質(zhì)序列信息。白質(zhì)序列信息。r 3. 序列文件的標(biāo)識(shí)符：序列文件的標(biāo)識(shí)符：r DNA/RNA序列，序列，NM_XXXXXX；r 蛋白質(zhì)序列：蛋白質(zhì)序列：NP_XXXXXXBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics

9、, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. /sites/entrez?db=gener 2. 序列從序列從Refseq數(shù)據(jù)庫中得到數(shù)據(jù)庫中得到;r 3. 詳盡的注釋信息，包括基因在基因組的定位，基因詳盡的注釋信息，包括基因在基因組的定位，基因名稱、蛋白質(zhì)名稱，基因結(jié)構(gòu)，等等。名稱、蛋白質(zhì)名稱，基因結(jié)構(gòu)，等等。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-

10、2010, Semester 1, Soochowr 1. 專家審核的蛋白質(zhì)序列數(shù)據(jù)與知識(shí)庫；專家審核的蛋白質(zhì)序列數(shù)據(jù)與知識(shí)庫；r 2. UniProt Knowledgebase：Release 12.1，2019.08r 3. 包括：包括：r Swiss-Prot Release 54.1 of 21-Aug-2019: 277883 entries;r TrEMBL Release 37.1 of 21-Aug-2019: 4754787 entriesBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2

11、010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. DNA/RNA/氨基酸代碼的標(biāo)識(shí)氨基酸代碼的標(biāo)識(shí)r 2. GenBank數(shù)據(jù)格式數(shù)據(jù)格式r 3. UniProtr 4. FASTABioinformatics, 2009-

12、2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowDefinition: 標(biāo)題標(biāo)題序列長度序列長度數(shù)據(jù)類型數(shù)據(jù)類型Accession number版本號(hào)版本號(hào)GI numberBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, S

13、emester 1, SoochowAccession numberBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 某天，某天，Prof. Gene發(fā)現(xiàn)人的發(fā)現(xiàn)人的Hela細(xì)胞中，有絲分裂細(xì)胞中，有絲分裂期間有異常情況：細(xì)胞不再分裂，而是開始凋亡期間有異常情況：細(xì)胞不再分裂，

14、而是開始凋亡(表表型，型，phenotype)，通過實(shí)驗(yàn)的方法，通過實(shí)驗(yàn)的方法(例如，酵母雙雜例如，酵母雙雜交交)，發(fā)現(xiàn)了與有絲分裂期間某個(gè)蛋白可能相互作用，發(fā)現(xiàn)了與有絲分裂期間某個(gè)蛋白可能相互作用的一個(gè)基因，測序結(jié)果如下的一個(gè)基因，測序結(jié)果如下(genotype)：CCCCTGCCTGGCAGCCCTTTCTCAAGGACCACCGCATCTCTACATTCAAGAACTGGCCCTTCTTGGAGGGCTGCGCCTGCACCCCGGAGCGGATGGCCGAGGCTGGCTTCATCCACTGCCCCACTGAGAACGAGCCAGACTTGGCCCAGTGTTTCTTCTGCTTCAA

15、GGAGCTGGAAGGCTGGGAGCCAGATGACGACCCCATAGAGGAACATAAAAAGCATTCGTCCGGTTGCGCTTTCCTTTCTGTCAAGAAGCAGTTTGAAGAATTAACCCTTGGTGAATTTTTGAAACTGGACAGAGAAAGAGCCAAGAACAAAATTGCAAAGGAAACCAACAATAAGAAGAAAGAATTTGAGGAAACTGCGGAGAAAGTGCGCCGTGCCATCGAGCAGCTGGCTGCCATGGATTGAGGCCTCTGGCBioinformatics, 2009-2010, Semester 1, Soochow

16、Bioinformatics, 2009-2010, Semester 1, Soochowr 1. 這是哪個(gè)基因？這是哪個(gè)基因？r 2. 編碼的蛋白質(zhì)序列是怎樣的？編碼的蛋白質(zhì)序列是怎樣的？r 3. 有沒有保守的功能結(jié)構(gòu)域有沒有保守的功能結(jié)構(gòu)域 (domain)？r 4. 它的功能是怎樣的？它的功能是怎樣的？r 5. 它在真核生物中保守嗎？它在真核生物中保守嗎？r 6. 有沒有三級(jí)結(jié)構(gòu)信息？有沒有三級(jí)結(jié)構(gòu)信息？Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochow

17、/Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochow輸入序列輸入序列Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soocho

18、wBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowUniGeneGeo: 基因表達(dá)信息基因表達(dá)信息Gene info：基因信息：基因信息Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010,

19、 Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. 該基因?yàn)槿说脑摶驗(yàn)槿说腟urvivin基因，染色體定基因，染色體定位：位：17號(hào)染色體，號(hào)染色體，73721872-73733311；基；基因標(biāo)識(shí)符：因標(biāo)識(shí)符：NM_001168.

20、2;r 2. 初步的功能分析：細(xì)胞周期，初步的功能分析：細(xì)胞周期，caspase酶酶的抑制因子，等等。的抑制因子，等等。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinforma

21、tics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 人的人的Survivin蛋白質(zhì)包含蛋白質(zhì)包含142個(gè)氨基酸，序個(gè)氨基酸，序列標(biāo)識(shí)符為：列標(biāo)識(shí)符為：NP_001159.2Bioinformatics, 20

22、09-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soo

23、chowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr Survivin具有保守的功能結(jié)構(gòu)域具有保守的功能結(jié)構(gòu)域BIRBioinformatics, 2009-2010, Semest

24、er 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformat

25、ics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 1. 在瘤形成過程中可能起一定作用；在瘤形成過程中可能起一定作用；r 2. 阻礙阻礙G2/M期的細(xì)胞編程性凋亡；期的細(xì)胞編程性凋亡；r 3. Chromoso

26、mal passenger complex (CPC)的成員之一。的成員之一。r r 細(xì)胞亞定位：胞質(zhì)，核。細(xì)胞亞定位：胞質(zhì)，核。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioin

27、formatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Se

28、mester 1, Soochowr 人的人的Survivin在酵母中的同源物可能是在酵母中的同源物可能是BIR1。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformati

29、cs, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 如今，如今，Prof. Gene知道了：知道了：r 1. 該基因?yàn)槿说脑摶驗(yàn)槿说腟urvivin基因，染色體定位：基因，染色體定位：17號(hào)染色體，號(hào)染色體，73721872-73733311；基因標(biāo)識(shí)符：；基因標(biāo)識(shí)符：NM_001168.2;r 2. 人的人的Survivin蛋白質(zhì)包含蛋白質(zhì)包含142個(gè)氨基酸，序列標(biāo)識(shí)符為：個(gè)氨基酸，序列標(biāo)

30、識(shí)符為：NP_001159.2r 3. Survivin具有保守的功能結(jié)構(gòu)域具有保守的功能結(jié)構(gòu)域BIRr 4. Survivin的細(xì)胞亞定位：胞質(zhì)，核，其功能有：的細(xì)胞亞定位：胞質(zhì)，核，其功能有：r (1) 在瘤形成過程中可能起一定作用；在瘤形成過程中可能起一定作用；r (2) 阻礙阻礙G2/M期的細(xì)胞編程性凋亡；期的細(xì)胞編程性凋亡；r (3) Chromosomal passenger complex (CPC)的成員之一。等等。的成員之一。等等。r 5. 人的人的Survivin在酵母中的同源物可能是在酵母中的同源物可能是BIR1。r 6. Survivin的三級(jí)結(jié)構(gòu)已知，在的三級(jí)結(jié)構(gòu)已知，在PDB中的標(biāo)識(shí)符為中的標(biāo)識(shí)符為1E31。Bioinformatics, 2009-2010, Semester 1, SoochowBioinformatics, 2009-2010, Semester 1, Soochowr 某天，某天，Prof. Gene在小