核酸与蛋白质的分析

1、YM-Bioinfo核酸與蛋白質的分析陽明大學 生物資訊學研究所楊 永 正YM-Bioinfo基因體計畫的衝擊/cgi/content/full/291/5507/1221/F1YM-Bioinfo基因體分析的精神宏觀分析 (global analysis)= 得到所有的資訊(與傳統上“由假說設計實驗”的方法不同)YM-BioinfoDNA 語言為何難懂? 5 10 15 20 25 30 35GARBA GEYOU THROW OUTJU NKYOU KEEPT HEREF 40 45 50 55 60 65 70ORE90 %OFTH EGE

2、NO MEISJ UNKSB RENNE RGarbage you throw out, junk you keep. Therefore, 90% of the Garbage you throw out, junk you keep. Therefore, 90% of the genome is junk. - S. Brenner.genome is junk. - S. Brenner.YM-Bioinfo語言的三大要素:字,詞與文法Hbscbhf zpv uispx pvu, kvolkvol zpv lffq. Uifsfgpsf,01 fg uif hfopnf jt kvol

3、kvol. =T. Csfoofs.Garbage you throw out, junk you keep. Therefore, Garbage you throw out, junk you keep. Therefore, 90% of the genome is junk. - S. Brenner.90% of the genome is junk. - S. Brenner.A-B, B-C, C-D, D-E, E-F, - etc.YM-Bioinfo語言學的類比LOCUS HSFF91B7B 780 bp DNA PRI 23-SEP-1999DEFINITION Huma

4、n DNA sequence from clone 91B7B on chromosome 22, complete sequence.ACCESSION AL118554 Z80773NID g5922693VERSION AL118554.1 GI:5922693KEYWORDS HTG.SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.REFEREN

5、CE 1 (bases 1 to 780) AUTHORS Hunt,A. TITLE Direct Submission JOURNAL Submitted (23-SEP-1999) Sanger Centre, Hinxton, Cambridgeshire, CB10 1SA, UK. E-mail enquiries: humquerysanger.ac.uk Clone requests: clonerequestsanger.ac.ukCOMMENT During sequence assembly data is compared from overlapping clones

6、. Where differences are found these are annotated as variations together with a note of the overlapping clone name. Note that the variation annotation may not be found in the sequence submission corresponding to the overlapping clone, as we submit sequences with only a small overlap as described abo

7、ve. The following abbreviations are used to associate primary accession numbers given in the feature table with their source databases: Em:, EMBL; Sw:, SWISSPROT; Tr:, TREMBL; Wp:, WORMPEP; Information on the WORMPEP database can be found at http:/www.sanger.ac.uk/Projects/C_elegans/wormpep IMPORTAN

8、T: This sequence is not the entire insert of clone 91B7. It may be shorter because we only sequence overlapping sections once, or longer because we arrange for a small overlap between neighbouring submissions. The true right end of clone cN121E8 is at 100 in this sequence. The true right end of clon

9、e fF91B7 is at 780 in this sequence. This sequence has been finished according to sequence map criteria as follows. An attempt is made to resolve all sequencing problems, such as compressions and repeats, but not necessarily within known annotated human repeat sequence elements (e.g. Alu). Where the

10、 sequence is ambiguous, there is an annotation using the unsure feature key. This sequence was generated from part of bacterial clone contigs of human chromosome 22, constructed by the Sanger Centre Chromosome 22 Mapping Group. Further information can be found at http:/www.sanger.ac.uk/HGP/Chr22 91B

11、7B is from the human chromosome 22-specific Fosmid library described in Kim U-J. et al Genet_Anal 12(2): 81-84, and is part of a cosmid contig isolated using YACs and markers from the Sanger Centre chromosome 22 YAC contig described in Collins, J.E. et al Nature 377 Suppl., 367-379. VECTOR: pFOS1.FE

12、ATURES Location/Qualifiers source 1.780 /organism=Homo sapiens /db_xref=taxon:9606 /chromosome=22 /clone=91B7BASE COUNT 156 a 199 c 213 g 212 tORIGIN 1 ctttgctgtg tctgtcccaa gaaatccaga caagaggcac aaagccggaa ggatgtgggc etc.Garbage you throw out, junk you keep. Therefore, 90% of the genome is junk. -

13、S. Brenner.Junk文法: 巨分子間的交互作用原則字詞生命之書YM-Bioinfo觀察歷史有助於了解時代趨勢發現DNA結構遺傳工程技術的建立人類基因體 分析計畫？數學、物理、化學、統計、電腦科學的整合195319731990YM-Bioinfo可解釋遺傳現象有一個具體的模型可以想像複製是怎麼進行的發現DNA雙螺旋結構的意義* The above picture was taken from :8001/esgbio/YM-Bioinfo如何複製出DNA序列的互補股序列?5-ATGGGAGAGAAGGCGCTG-3 YM-Bioinfo解 答

14、“人工”智慧 在”Word”中置換 (?)* 不要忘記倒置5-ATGGGAGAGAAGGCGCTG-33-TACCCTCTCTTCCGCGAC-55-CAGCGCCTTCTCTCCCAT-3YM-Bioinfo如果要將上千個鹼基變為互補股序列，該怎麼辦?請連到下列網址取序列/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&list_uids=214818&dopt=fastaYM-BioinfoEMBOSShttp:/bioportal.cgb.indiana.

15、edu/Pise/5.a/revseq.htmlYM-Bioinfo生物學的中心教條 (central dogma)DNARNA轉 錄轉 譯蛋白質YM-Bioinfo核酸定序遠比蛋白質定序容易YM-BioinfoSanger 定序法5 A T C T A G G-3 ddC-5 ddC-5 ddT-5 ddA-5 ddG-5 ddA-5 ddT-5deoxynucleosideYM-Bioinfo請將下列DNA序列轉錄為RNA序列，再轉譯為蛋白質序列?5-ATGGGAGAGAAGGCGCTG-3YM-Bioinfo解 答5-ATGGGAGAGAAGGCGCTG-35-AUGGGAGAGAAGG

16、CGCUG-3MGEKAL* Picture made from http:/www.kazusa.or.jp/java/codon_table_java/YM-Bioinfo所有的生物都用同樣的密碼表嗎?YM-Bioinfo解 答/Taxonomy/Utils/wprintgc.cgiYM-Bioinfo如果要將上千個鹼基轉譯為蛋白質序列，該怎麼辦?請連到下列網址取序列/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&

17、;list_uids=214818&dopt=fasta(只要轉譯42到1076即可)YM-BioinfoEMBOSS/Pise/5.a/transeq.htmlYM-Bioinfo有核酸序列很好，可是只有核酸序列可能不知道基因功能該怎麼辦?YM-Bioinfo利用功能來分離蛋白質ComponentsPurposeConcentrationCTP, GTP, UTPSubstrate0.15 mMa-14CATPLabeled substrate0.15 mMT4 phage DNATemplate20 ug/mlTris

18、7.9Buffer component40 mMMgCl2Buffer component10 mMEDTABuffer component0.1 mMb-mercaptoethanolBuffer component5.8 mMKClBuffer component150 mMBSABuffer component0.5 mg/mlProtein fractionsEnzymevariable amountYM-Bioinfo利用質譜儀定序molecular weight(M.W.)abundancyYM-Bioinfo如何利用蛋白質尋找核酸序列?請將蛋白質序列 ”MGEKAL”反轉譯為核酸

19、序列YM-BioinfoEMBOSS: backtranseq/Pise/5.a/backtranseq.htmlYM-Bioinfo將蛋白質序列反轉譯為核酸序列時，會產生甚麼問題?YM-Bioinfo解 答* Picture made from http:/www.kazusa.or.jp/java/codon_table_java/一個氨基酸可能對應到多個核酸密碼YM-BioinfoIUPAC 歧義字碼表/mdecode/images/iupac.htmlIUPAC Co

20、deMeaningComple-mentYC or TRKG or TMVA or C or GBHA or C or TDDA or G or THBC or G or TVNG or A or T or CNIUPAC CodeMeaningComple-mentAATCCGGGCT/UTAMA or CKRA or GYWA or TWSC or GSYM-Bioinfo知道部份的蛋白質序列，可能找到整個基因的核酸序列嗎?提示: 基因體計畫收集了許多核酸序列YM-BioinfoGenBank Divisions/Genbank/index.ht

21、mlOrganismal Divisions: BCT: Bacterial seq. PRI: Primate seq., include Human Phase 3 ROD: Rodent seq. MAM: Other mammalian seq. VRT: Other vertebrate seq. INV: Invertebrate seq., include Drosophila, C. elegans Phase 3 PLN: Plant and Fungal seq., include Arabidopsis Phase 3 VRL: Viral seq. PHG: Phage seq. RNA: Structural RNA seq. SYN: Synthetic and chimeric seq. UNA: Unannotated seq. Functional Divisions: EST: Expressed Seq. Tags STS: Seq