课程名称︰生物资讯学 课程性质︰选修 课程教师︰阮雪芬 开课学院：生科院 开课系所︰生科系 生技系 考试日期（年月日）︰08/4/15 考试时限（分钟）：take-home test, return on 4/22 是否需发放奖励金：是 （如未明确表示，则不予发放） 试题 : 1.What are the differences among the following three genome browsers(UCSC, NCBI, Ensembl)? (15%) 2.Obtain the TRANSFAC matrix representing the TATA box. Carefully read the content of the resord. how many sites were used to build this matrix? Report the process with SP1 and cEBP. how many sites were aligned to build their matrices? Is there any relationship between the quality of the predictions and the number of collected binding sites? (20%) 3.Using TRANSFAC programs MAINSPECTOR or MATCH, scan the promoter sequence using the full collection of vertabrate matrices. Identify the real binding sites in the output. (10%) 4.Select one interestng miRNA and use TargetScan to predict its target genes. (10%) 5.Access the two traces shown in Fig 7.1 from the NCBI TraceArchive by entering their ti number into the search box (ie.,215500760 and 220064691). Use the returned FASTA sequence and one of the search tool to find where these sequence align to the human genome. (30%) (1) Find the SNP shown in the figure. Which one has the same allele as the reference sequence. (2) From the base location in the trace that agree with reference sequence in 1, find the first base that does not agree. Would this be called a SNP, or not? Explain. (3) Do the same for the other trace, starting from the SNP location. Would this be called a SNP, or not? Explain. 6.How to apply bioinformatics approach to biomedical research? Please select one topic which impressedyou, and then describe it in detail. (15%) ps. the answer report should be returned on the 4/22 bioinformatics lecture --

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