課程名稱︰生物資訊學
課程性質︰選修
課程教師︰阮雪芬
開課學院：生科院
開課系所︰生科系 生技系
考試日期（年月日）︰08/4/15
考試時限（分鐘）：take-home test, return on 4/22
是否需發放獎勵金：是
（如未明確表示，則不予發放）
試題 :
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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