Exam 2 Study Guide
There are project-based questions on Exam 2 that covers material from Units 4 through 6. There is no time limit for the exam. For the Exam, please be able to:
- Acquire DNA and protein sequences from NCBI
- Analyze sequences with the following programs:
- BLAST
- PROMALS3D
- Simple Phylogeny
- Report obtained results
Exam questions are similar to homework questions.
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Question 1 of 4
1. Question
Use NCBI’s Protein database to acquire the protein sequences for alpha-globin in human (NCBI locus tag CAA23748.1). Perform the following for the protein: (7 points each)
• Use BLASTP to compare the amino acid sequence for each protein individually to the non-redundant protein sequences (nr) database
• Use PSI-BLAST to compare the amino acid sequence for each protein individually to the non-redundant protein sequences (nr) database-
From the first iteration of PSI-BLAST results comparing the human alpha-globin to the non-redundant protein sequences (nr) database, what was the E-value of the hemoglobin subunit alpha protein found in Rhinopithecus roxellana?
From the first iteration of PSI-BLAST results comparing the human alpha-globin protein to the non-redundant protein sequences (nr) database, what was the percent identity of the hemoglobin subunit alpha protein found in Rhinopithecus roxellana?
From the first iteration of PSI-BLAST results comparing the human alpha-globin protein to the non-redundant protein sequences (nr) database, are the results the same or different from those obtained from BLASTP results?
From the second iteration of PSI-BLAST results comparing the human alpha-globin protein to the non-redundant protein sequences (nr) database, what was the percent identity of the hemoglobin subunit alpha protein found in Camelus dromedarius?
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Question 2 of 4
2. Question
Use NCBI’s Protein database to acquire the protein sequences for alpha-globin in human, grivet, tufted capuchin, mouse, carp, and goat (NCBI locus tags CAA23748.1, 731485A, 732177A, CAA24095.1, BAA20512.1, and CAA28435.1, respectively). Use PROMALS3D to perform a multiple sequence alignment on these sequences. (7 points each)
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From the PROMALS3D results, how many representative sequences are there?
From the PROMALS3D results, which representative sequence has sequences with black names directly under it indicating they are part of the same pre-aligned group?
From the PROMALS3D results above, how many conserved alpha-helix secondary structures were predicted?
From the PROMALS3D results above, how many conserved beta-strand secondary structures were predicted?
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Question 3 of 4
3. Question
Use the CLUSTALW output of the multiple sequence alignment to construct a phylogenetic tree using Simply Phylogeny. (8 points each unless otherwise noted)
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Based on the phylogenetic tree, which species is closest species to human? Provide your answer as a NCBI locus tag.
Based on the phylogenetic tree, which species is the second closest species to human? Provide your answer as a NCBI locus tag.
Based on the phylogenetic tree, which 2 species are the furthest species from human? Provide your answer as NCBI locus tags in alphabetical order. (16 points)
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Question 4 of 4
4. Question
Answer the following questions from these PROMALS3D results (4 points each):
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From the PROMALS3D results above, which sequence is the representative sequence?
From the PROMALS3D results above, how many conserved alpha-helix secondary structures were predicted?
From the PROMALS3D results above, how many conserved beta-strand secondary structures were predicted?
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