RDP4軟件分析指南

1、重組檢測軟件RDP4的應(yīng)用匯報(bào)人：趙燁I(lǐng)ntroduction RDP4 (Recombination Detection Program version 4) 是一個(gè)檢測和分析重組信號的軟件，包括7種基本檢測程序（RDP method, GENECONV, Bootscanning, MaxChi, Cimaera, 3SEQ and SiScan）和4種附加檢測程序（LARD, PHYLPRO, distance plots and TOPAL）。操作基本步驟 打開一個(gè).meg格式的文件：左擊鼠標(biāo)open按鈕。 點(diǎn)擊頁面頂端options按鈕，進(jìn)入General頁面選擇一系列參數(shù)： 左擊主

2、界面上的X-over按鈕開始進(jìn)行重組分析。 分析完畢后出現(xiàn)四個(gè)界面，順時(shí)針方向依次為： Sequence display The recombination information display Schematic sequence display Plot displayRecord significant evidenceof recom binationM ove a sliding window acrosssub-sequence and calculate pairwise identities M ultiple sequence alignm entSelect three

3、sequencesand discard all non-inform ative sitesInform ation-rich sub-sequenceCheck for evidence of recom binationCalculate significance where: G is the total num ber of of possible sequence tripletsL is the Length of the sequenceN is the length of the putatively recom binant regionm is the proportio

4、n of nucleotides in com m on between the putative recom binant and parental sequences in the recom biant regionp is the proportion of nucleotides in com m on between the putative recom binant and parental sequences in the entire sequence.Repeat with the nextthree sequences( )P=N!m !(N-m )!pNX(1-p)N-

5、mXLNm = MNG XAACGCGATTGCAGGAAGGCATATGTTATGGCATAAGGCGATAGCAGGTGGCCTTACATTATGGCATAAGGCGATTCCTGGAAGCCTTACGTAATGGCATAAGGTGATAGCAGGTAGCCTTACATAATCGCATAAGGCGATAGCAGGTAGGCTTACGTTATCGCATAAGGCGATAGCAGGTAGGCTTATATTACGGCATGTCTACTCGATCTGAAGATGTTGAGATGTTATCA1760152122823043Position in alignm ent1.00.50.0Pairwise

6、 identity1.07 X 101.07 X 10- -6 6Positions of inform ative sitesPotential recom binant regionM ajor parent : recom binant plotM inor parent : recom binant plotM inor parent : m ajor parent plotP-Value1760152122823043Position in alignm ent1.00.50.01760152122823043Position in alignm ent1.00.50.0Pairwi

7、se identity1.07 X 101.07 X 10- -6 6Positions of inform ative sitesPotential recom binant regionM ajor parent : recom binant plotM inor parent : recom binant plotM inor parent : m ajor parent plotP-ValueFigure 8. The original RDP m ethod. AThe analysis procedure. BAn exam ple pairwise identity plot.B

8、Record significant evidenceof recom binationM ove a sliding window acrosssub-sequence and calculate pairwise identities M ultiple sequence alignm entSelect three sequencesand discard all non-inform ative sitesInform ation-rich sub-sequenceCheck for evidence of recom binationCalculate significance wh

9、ere: G is the total num ber of of possible sequence tripletsL is the Length of the sequenceN is the length of the putatively recom binant regionm is the proportion of nucleotides in com m on between the putative recom binant and parental sequences in the recom biant regionp is the proportion of nucl

10、eotides in com m on between the putative recom binant and parental sequences in the entire sequence.Repeat with the nextthree sequences( )P=N!m !(N-m )!pNX(1-p)N-mXLNm = MNG XAACGCGATTGCAGGAAGGCATATGTTATGGCATAAGGCGATAGCAGGTGGCCTTACATTATGGCATAAGGCGATTCCTGGAAGCCTTACGTAATGGCATAAGGTGATAGCAGGTAGCCTTACATA

11、ATCGCATAAGGCGATAGCAGGTAGGCTTACGTTATCGCATAAGGCGATAGCAGGTAGGCTTATATTACGGCATAACGCGATTGCAGGAAGGCATATGTTATGGCATAAGGCGATAGCAGGTGGCCTTACATTATGGCATAAGGCGATTCCTGGAAGCCTTACGTAATGGCATAAGGTGATAGCAGGTAGCCTTACATAATCGCATAAGGCGATAGCAGGTAGGCTTACGTTATCGCATAAGGCGATAGCAGGTAGGCTTATATTACGGCATGTCTACTCGATCTGAAGATGTTGAGATGT

12、TATCGTCTACTCGATCTGAAGATGTTGAGATGTTATCA1760152122823043Position in alignm ent1.00.50.0Pairwise identity1.07 X 101.07 X 10- -6 6Positions of inform ative sitesPotential recom binant regionM ajor parent : recom binant plotM inor parent : recom binant plotM inor parent : m ajor parent plotP-Value1760152

13、122823043Position in alignm ent1.00.50.01760152122823043Position in alignm ent1.00.50.0Pairwise identity1.07 X 101.07 X 10- -6 6Positions of inform ative sitesPotential recom binant regionM ajor parent : recom binant plotM inor parent : recom binant plotM inor parent : m ajor parent plotP-ValueFigur

14、e 8. The original RDP m ethod. AThe analysis procedure. BAn exam ple pairwise identity plot.BFigure 1. The main components of the RDP interface. Command buttons 命令按鈕Tree display 進(jìn)化樹顯示Matrix display 矩陣顯示Recombination info. Display重組信息顯示Sequence display 序列顯示Plot display繪圖顯示Schematic sequence display圖解

15、序列顯示Identity display 同源性顯示 RDP4界面的主要組成部分界面的主要組成部分分析進(jìn)度條Position indicator位點(diǎn)指示Identity display同源性顯示Sequence display序列顯示Sequence namesToggle sequence displayIdentity indicatorToggle identity displaysequence display. 左擊序列中的部位可以顯示不同顏色代表的含義鼠標(biāo)懸空在某個(gè)核苷酸上會顯示出該核苷酸處于何序列的具體位置右擊鼠標(biāo)可以保存不同形式你想要的序列Warnings and additi

16、onalmethod specific info.P-Value sProbable recombinant (recombinant) and parental sequencesBreakpoint positions: Insequence (in alignment)Method used to detectrecombinant regionThe recombination information display現(xiàn)以下情況，該界面還會出現(xiàn)warning標(biāo)示（紅色）：（1）在比對序列中只有一個(gè)可能為父母代毒株的序列（2）有可能(約30%或更大的可能)誤認(rèn)為重組序列(即實(shí)際上父母代的序

17、列中的某個(gè)才是真正的重組毒株)如果是這樣會在后面顯示出實(shí)際上可能為重組毒株的父母代毒株的名字。（3）無法識別出一個(gè)或全部兩個(gè)突變位點(diǎn)。（4）一個(gè)或兩個(gè)突變位點(diǎn)是錯(cuò)位的。（5）重組信號微弱（6）如果復(fù)合信號可能是一個(gè)分析錯(cuò)誤的人工制品?！癱onfirmation table”部分表明了用不同方法檢測出發(fā)生該重組事件的毒株數(shù)和關(guān)于目前檢測到的重組事件的符合程度Confirmation table 下面是一個(gè)總結(jié)性的柱狀圖，對于99%的用戶來說前三條柱狀圖代表的是有用的信息。柱狀圖下面的分?jǐn)?shù)大于60%代表這該毒株幾乎確定為重組毒株。大于40%小于60%的分?jǐn)?shù)代表軟件可能犯了錯(cuò)誤，但也可能沒有。小于4

18、0%表示該毒株很可能不是重組毒株。The schematic sequence displayCurrent viewCycle through display options 改變視圖顏色Recombinant region 重組區(qū)域Background sequence 背景序列主要親本與重組序列的同源性潛在的重組區(qū)域P-value次要親本與重組序列的同源性主要親本與次要親本的同源性The Plot Display“Recombinant” sequence“Parental” sequencesPortion of alignmentused to draw tree Cycle through treesView all trees SimultaneouslySwitch to recombinationinformation displaySwitch to compatibilitymatrix displayFigure 6. The dendrogram display. KeyScale barTree Display點(diǎn)擊右上角的“cycle th