Midterm Exam

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Find the BEST Match for Each Genomic Term (2 Points Each) 1. _f_ Homologue 2. _c_ Minimum Tiling Path 3. _i_ Chromosome Walking 4. _h_ E-value 5. _l_ Genbank 6. _d_ Segmental Duplication 7. _n_ Tandem Duplication 8. _a_ Phrap 9. _g_ Syntenic 10. _e_ Colinear a. A program that finds overlapping regions in sequencing data b. A program that calculates the strength of evidence for each basecall as part of DNA sequencing c. Order of clones that most efficiently covers a genome region d. Multiple copies of a genome region derived from ancient genome rearrangement(s) e. Sequences in the same linear order in two or more taxa f. Sequences that share a common ancestor g. Sequences physically linked to one another in two or more taxa h. Probability of finding an alignment with a given Blast score i. Gene cloning based on a marker located close to a target, followed by searching for clones progressively closer j. Gene cloning based on isolating mRNA & cDNAs coming from a tissue or treatment of interest k. A database of conserved protein sequence motifs l. A database of all public nucleotide and protein sequences m. Related sequences separated from one another by duplication n. Multiple copies of a genome region located adjacent to one another 2
Short Answer (8 points each) — Use Only the Space Provided! 1. What is the difference between an unknown protein and a hypothetical protein? A “hypothetical” protein is a predicted entity never before seen in nature. A hypothetical protein is predicted directly from genome sequence by one of many computer algorithms that search for sequence regions that have the hallmarks of protein-coding genes. By contrast, an “unknown” protein is known to exist in nature because its corresponding mRNA has been observed at least once, either in a targeted cDNA study or as part of an EST project. 2. Imagine you have been invited to a local high school to talk to students about genomics. The very first student asks “So, what is genomics anyway?” How do you answer? There is no one correct definition for genomics. A good answer would include the following features: A perspective on biology in which all of the genes or gene products are viewed together to reveal interesting or important properties. Genomics is based on massive amounts of DNA sequence data and requires the use of high powered computer tools. 3. Assume that you’ve used the program FPC to construct the BAC contig map shown below. What additional steps would you use to validate the map – and do so in a highly efficient manner. (Use any of the genomic/molecular techniques we’ve talked about in class plus those you’ve learned about in other classes.) 29F19 84J03 19B16 65J15 A BAC contig map, such as the one displayed here, would typically be constructed by DNA fingerprinting and the use of an algorithm such as FPC. This approach is usually effective at discovering BAC clones that overlap one another, but it frequently makes errors about the exact order or the degree of overlap. Before using such a physical map as a basis for generating a minumum tiling path (and subsequent DNA sequencing), scientists frequently sequence just the ends of BAC clones and use this information to generate probes/PCR primers from those BAC-ends. The probes and PCR primers can then be used to determine whether other BAC clones in the physical map really do have the predicted orientation through a combination of Southern blotting and PCR amplification. 4. Briefly compare and contrast BAC-by-BAC versus Shotgun genome sequencing. Be sure to illustrate the advantages and disadvantages of both. (10 points) A BAC-by-BAC approach to genome sequencing begins with the construction of a detailed genetic mapping (segregation analysis) and physical mapping (fingerprint/FPC of BAC clones). These maps provide the basis for predicting a minimum tiling path of BAC clones, typically verified through BAC-end sequencing. The chosen BAC clones are 3
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Page 5 and 6: Look at this BLAST report below and

Midterm Exam

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