最新大规模基因组测序中的信息分析PPT课件.ppt

《最新大规模基因组测序中的信息分析PPT课件.ppt》由会员分享，可在线阅读，更多相关《最新大规模基因组测序中的信息分析PPT课件.ppt（26页珍藏版）》请在淘文阁 - 分享文档赚钱的网站上搜索。

1、大规模基因组测序中的信息分析大规模基因组测序中的信息分析Fractal dimension of exon and intron We introduce the mapping from nucleotide sequences to two-dimensional metric space by assigning each nucleotide a fixed vector and constructing a representation by joining these vectors end-to-end.Fractal Dimension of Exon and Intron S

2、equencesD is the fractal dimension and there exists self-similarity in this rangeof the nucleotide sequence.-CGCGGCGTGTGTTATA-0 0.5 1 1.5 2 2.5 3 3.5 07654321Intron Seq.Exon Seq.Random Seq.End-to-end RangeMain RangeGeometric RangelnN and are average of and of each class of sequences,and are their st

3、andard deviations.The class of exon sequences is denoted as EX,and intron sequences IN,randomized exon sequences RE,and randomized intron sequences RI.Complexity analysis In our case complexity means that how many patterns of base connections are there in a window,which are from different parts of D

4、NA sequences.Our results show that the complexity of exon is larger than the complexity of intron and 5-flanking and 3-flanking.Relative Complexity in Exon,Intron and FlanksRelative Complexity in Exon,Intron and Flanks Using the methods and techniques in cryptology One could think that the DNA seque

5、nces are similar with the telegram,which has been used to transmit secrets in the field of commerce or military affairs,so we try to apply methods and techniques in cryptology to DNA sequence analysis.l As the first step we introduce some parameters of cryptology to DNA sequence analysis.Coincident

6、index In cryptology this parameter has been used to find the plain code in an enciphered text of a telegram.The part with the plain code is the high-value region of this parameter.We assume that exon is corresponding to the plain code and also has the high-value of the coincident index.Unicity dista

7、nceCOINCIDENT INDEX OF EXON AND INTRONThe original presentation of coincident index is:in which N is the number of characters in the sequence,L is the number of different kinds of character,and is the frequency of the lth character appearing in this sequence.The coincident index introduced from cryp

8、tology is applied to DNA sequence analysis.In case of mono-letter,the expressing of coincident index IC of DNA sequence is:j=0,1,.,L-1;k=A,C,G,T.R=4 25 (25 1)=2400 In case of biletter,the expression of IC is:j=0,1,.,L-1;k=AA,AC,AG,AT,CA,CC,.TG,TTThe Values of Coincident Index in HSHSC70 SequenceThe

9、Values of Coincident Index in HSHSC70 SequenceORF Prediction of the Contig by 5 MethodORF Prediction of the Contig by 5 MethodComposite Artificial Neural Network SystemAuto-annotation ProcedureA.T.tengcongensis Complete Genome AnalysislThe bacteria was designated as Thermoanaerobacter tengcongensis

10、MB4 which was isolated from the hotspring in Tengcong area,Yunnan Province of China,by the scientists working in the institute of microbiology of Chinese Academy of Sciences four years ago.The cell morphology of the bacteria is baculiform,Gram reaction is negative(-),it can not form spore and also c

11、an not mobilize.The bacteria is anaerobes to oxygen tolerance,optimum temperature is 75oC,optimum pH 7.0.lThe genome of T.tengcongensis consists of a single circular chromosome of 2,689,441 base pairs(bp)with an average of 37.6%G+C content.大规模全基因组shotgun测序Shotgun 反应:109,970有效总读长：26,553,803bp基因组总长：2,689,445bp冗余度：9.87PCR补洞PCR反应：40,000PCR产物测序：4,100Circular representation of the genome of T.tengcongensis MB4 谢谢各位!