Homework 2: Fill in the blank – 3 points each unless otherwise noted – capitalization does not matter. Students can take this assignment an unlimited number of times with the best score kept.
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Acquire the complete genome for the Zika virus in NCBI (NCBI Reference Sequence: NC_012532). Identify all the protein-coding regions in that sequence using NCBI’s ORF-Finder. From this program’s output, please answer the following questions:
- How many ORFs were found if nested ORFs were NOT ignored?
- How many ORFs were found if nested ORFs were ignored?
- For the ORFs found when nested ORFs were ignored, what are the first 10 amino acids for the protein sequence for ORF4?
Acquire the complete genome for the Human mitochondrial reference genome in NCBI (NCBI Reference Sequence: NC_012920). Identify all the protein-coding regions in that sequence using NCBI’s ORF-Finder. From this program’s output, please answer the following questions:Â
- How many base pairs (bp) is the genome?
- How many ORFs were found if nested ORFs were ignored?
- For the ORFs found when nested ORFs were ignored, how many ORFs are located on the positive strand (HINT: Use the Mark subset feature)?
- For the ORFs found when nested ORFs were ignored, how many amino acids long is ORF33?
Analyze the Human mitochondrial reference genome from NCBI (NCBI Reference Sequence: NC_012920) with tRNAscan-SE. From this program’s output, please answer the following questions:
- How many tRNAs were identified?
- Which amino acids had more than one coding region? Use three letter abbreviations and list amino acids in alphabetical order separated by a comma.
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