1、YM-Bioinfo核酸與蛋白質的分析 (II)陽明大學 生物資訊學研究所楊 永 正YM-Bioinfo上次課程複習 emboss程式簡介 Revseq: 互補、倒置 Transeq: 轉譯 Backtranseq: 反轉譯 (可能產生多條序列) 密碼表 基因體資訊存於GenBank YM-Bioinfo反轉譯出的核酸序列可能與原序列不同* Picture made from http:/www.kazusa.or.jp/java/codon_table_java/MGEKAL5-ATGGGC CGAGAAGGCC CCTG -35-ATGGGAGAGAAGGCGCTG-3YM-Bioinfo

2、反轉譯出的核酸序列與原序列不同， 是否可在Genbank中找到原序列?5-ATGGGCGAGAAGGCCCTG-3YM-Bioinfo提 示使用資料庫搜尋程式blastn/BLAST/YM-BioinfoSubmit sequence for blast analysisYM-BioinfoFormat blast resultYM-BioinfoWait for resultsYM-BioinfoBlastn resultsYM-BioinfoSearch for short, nearly exact matchesYM-Bioinfo反轉譯出的

3、核酸序列，在Genbank中不找到原序列。 該怎麼辦?必須有更長的序列(請回去後做習題組，在週一上午上課前將結果寄到.tw)YM-Bioinfo上述序列是來自於 Xenopus laevis的TFIIIA 基因，如何才能查到此序列?關鍵字查詢: Xenoups, TFIIIA/YM-Bioinfo有了整個基因的核酸序列，要怎麼找相似的基因?利用非洲水生蛙的TFIIIA基因，找其他生物的TFIIIA基因，或與TFIIIA相似的基因YM-Bioinfo提 示先找到Xenopus laevis之TFIIIA蛋白質序列再使用資料庫搜尋程

4、式blastp/BLAST/YM-Bioinfo解答 尋找序列YM-Bioinfo解 答 - blastpYM-BioinfoYM-BioinfoYM-BioinfoYM-Bioinfo若想知道TFIIIA 蛋白質中是否有蛋白質模組樣式(pattern)，應使用哪一個程式分析? /emboss/YM-Bioinfo解 答/Pise/5.a/patmatmotifs.htmlYM-Bioinfo甚麼是 ZINC_FINGER_C2

5、H2_1?提示: 請在網路上尋找Prosite資料庫中，鋅指(zinc finger)模組的說明。 YM-Bioinfo鋅指(zinc finger)模組的發現 Miller, J., McLachlan, A.D., and Klug, A. (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO 4, 1609-1614., contains an unusually large number of Cys and His resid

6、ues. At first sight these residues appeared to us to form roughly periodic groupings. We therefore made a systematic search for repeats in both amino acid sequence and the cDNA, using the diagonal comparison matrix method and the damped Needleman and Wunsch method (see Materials and methods).YM-Bioi

7、nfoDiagonal MatrixMethod A T G C G G C G T A C T G A CA 1 1 1T 1 1 1G 1 1 1 1 1C 1 1 1 1G 1 1 1 1G 1 1 1C 1 1 1G 1 1T 1 1A 1 1C 1 1T 1G 1A 1C 1identical = 1different = emptyOff Diagonal Line Represents Repeat within sequence analyzedYM-BioinfoScoringNucleic Acid Identical: 1 Different: 0Amino Acid b

8、losum62 MatrixYM-Bioinfo在Emboss套組中是否有繪製dotplot 的程式? /emboss/YM-Bioinfo解 答/Pise/5.a/dotmatcher.htmlYM-Bioinfo甚麼是window size與threshold?YM-BioinfoWindowWindow Size = 588, 96, 92, 74, 56, 66, 85, 97, 82, 77 81, 77, 75, 76, 77, 81YM-BioinfoThr

9、eshold88, 96, 92, 74, 56, 66, 85, 97, 82, 77Threshold = 7901, 01, 01, 00, 00, 00, 01, 01, 01, 00YM-Bioinfo三維示意圖 Diagonal Matrix PlaneThresholdScoreYM-Bioinfo在dotplot 上可以看到多少個鋅指模組? 提示: 試調整Window size 與Threshold YM-Bioinfo討 論該如何讀取相似的位置?YM-BioinfoYM-BioinfoHow to read a dot matrix plot?189241282230YM-B

10、ioinfoWhat is the pattern of repeats?YM-Bioinfo基因的特徵:分子解剖學YM-Bioinfo基因的調控:分子生物學YM-Bioinfo蛋白質可以辨識核酸序列噬菌體的抑制子與其操作子之間的交互作用。(Taken from http:/www4.oup.co.uk/best.textbooks/biochemistry/genesvii/ illustrations/ for educational purpose)YM-Bioinfo怎樣尋找可能的蛋白質接合位置?如果一個蛋白質可以調控多個基因，這些基因應有相似的蛋白質接合位置YM-Bioinfo解 答

11、由“MGEKAL”反轉譯出的核酸序列在Genbank中會找到多少相似的序列?YM-BioinfoEMBOSS: fuzznuc/Pise/5.a/fuzznuc.htmlYM-Bioinfo使用 IUPAC密碼對照表 N代表任何核苷酸 表示，例如 表示此位置，例如 . Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses. For example: ACG sta

12、nds for A or C or G. Ambiguities are also indicated by listing between a pair of curly brackets the nucleotides that are not accepted at a given position. For example: AG stands for any nucleotides except A and G. Each element in a pattern is separated from its neighbor by a -. (Optional in fuzznuc)

13、. Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: N(3) corresponds to N-N-N, N(2,4) corresponds to N-N or N-N-N or N-N-N-N. When a pattern is restricted to either the 5 or 3 end of a sequence, that pattern either starts with a symbol. A period ends the pattern. (Optional in fuzznuc). For example, CG(5)TGAN(1,5)CYM-Bioinfo# Program: fuzznuc# Rundate: Sat May 14 08:45:47 2005# Report_format: seqtable# Report_file: outfile.ou