Exam 1 Study Guide
There are project-based questions on Exam 1 that covers material from Units 1 through 3. There is no time limit for the exam. For the Exam, please be able to:
- Match the NCBI resource with its description
- Acquire DNA and protein sequences from NCBI
- Analyze sequences with the following programs:
- ORF-Finder
- tRNAscan-SE
- Softberry MolQuest
- Report obtained results
Exam questions are similar to homework questions.
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Question 1 of 4
1. Question
Match the NCBI resource with its description: 3 points each
- DNA and RNA sequences from GenBank and RefSeq
- Taxonomic classification and nomenclature catalog
- Genome sequencing projects by organism
- Collected information about gene loci
- Functional genomics studies
- Short genetic variations
- Human variations of clinical significance
- Protein sequences from GenBank and RefSeq
- Scientific and medical abstracts/citations
- Genotype/phenotype interaction studies
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- Gene
- Gene Expression Omnibus
- Pubmed
- Protein
- Genome
- Taxonomy
- dbSNP
- Nucleotide
- ClinVar
- dbGaP
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Question 2 of 4
2. Question
Acquire the complete mitochondrion genome for Mus musculus from NCBI (NCBI Reference Sequence: NC_005089.1). Identify protein-coding regions in that sequence using NCBI’s ORF-Finder. From this program’s output, please answer the following questions: (5 points each)
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1. How many base pairs (bp) is the genome?
2. How many ORFs were found if nested ORFs were ignored?
3. For the ORFs found when nested ORFs were ignored, how many ORFs are located on the negative strand?
4. For the ORFs found when nested ORFs were ignored, how many amino acids long is ORF5?
5. For the ORFs found when nested ORFs were ignored, what are the first 10 amino acids for the protein sequence for ORF5?
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Question 3 of 4
3. Question
Analyze the mitochondrion genome for Mus musculus with tRNAscan-SE. From this program’s output, please answer the following questions:
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- How many tRNAs were identified? (5 points)
- Which amino acids had more than one coding region? Use three letter abbreviations and list amino acids in alphabetical order separated by a comma. (10 points)
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Question 4 of 4
4. Question
Acquire the complete genomic sequence of Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, NCBI Reference Sequence: NC_002127.1, from NCBI. Use this sequence to perform the following: (5 points each)
- Use fgenesB from Softberry for bacterial operon and gene prediction
- Use BPROM from Softberry for prediction of bacterial promoters
- Use FindTerm from Softberry for finding terminators in bacterial genomes
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From the fgenesB results, how many genes were predicted from this sequence?
From the fgenesB results, how many transcription units were predicted from this sequence?
From the fgenesB results, how many operons were predicted from this sequence?
From the BPROM results, how many promoters were predicted from this sequence?
From the FindTerm results, what is the best terminator score for the sequence?
From the FindTerm results, what is the length of the best terminator in base pairs?
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