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Question 1 of 6
1. Question
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Acquire the complete mitochondrion genome for Felis catus from NCBI (NCBI Reference Sequence: NC_001700.1). Analyze the mitochondrion genome with tRNAscan-SE. From this program’s output, how many tRNAs were identified?
Identify protein-coding regions in the mitochondrion genome using NCBI’s ORF-Finder. From this program’s output, please answer the following questions:
• 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 negative strand?
• For the ORFs found when nested ORFs were ignored, how many amino acids long is ORF17?
• For the ORFs found when nested ORFs were ignored, what are the first 10 amino acids for the protein sequence for ORF17?
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Question 2 of 6
2. Question
Analyze the amino acid sequence for ORF17 using the appropriate programs to answer the provided questions:
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From PSORT results, ORF17 is most commonly predicted to be a(n) ___ protein. HINT: Check the comments section for identified nearest neighbors.
From InterPro results, what is the identifier (i.e., PF######) for the domain identified by the Pfam database?
From Phyre2 results, what was the confidence of the ORF17 model prediction as a percentage?
From Phyre2 results, what percent identity did the top template have for the model prediction?
From STITCH/STRING results, which of the highest confidence proteins was found by both STITCH and STRING? , (2 points each)
What molecule weighing 665.4 g/mol was found by STITCH but not STRING?
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Question 3 of 6
3. Question
Perform a BLASTP search comparing the amino acid sequence for ORF17 to the non-redundant protein sequences (nr) database. From this program’s output, please answer the following questions:
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• What is the identity of ORF17?
• What is the Accession number for the top BLASTP sequence identified?
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Question 4 of 6
4. Question
Use NCBI’s Protein database to acquire the protein sequences for cytochrome c oxidase subunit 1 in human, Klebsormidium nitens, Streptomyces rochei, Pseudomonas sp. RtIB026, and mouse (NCBI locus tags BAA07292.1, GAQ93836.1, BBC94614.1, BCJ04329.1, and CAD54434.1, respectively). Alongside ORF17, use PROMALS3D to perform a multiple sequence alignment on these 6 sequences.
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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 beta-strand secondary structures were predicted?
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Question 5 of 6
5. Question
Use the CLUSTALW output of the multiple sequence alignment to construct a phylogenetic tree using Simply Phylogeny.
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Based on the phylogenetic tree, which species is closest species to Felis catus ORF17? Provide your answer as a NCBI locus tag.
Based on the phylogenetic tree, which species is the furthest species from Felis catus ORF17? Provide your answer as NCBI locus tag.
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Question 6 of 6
6. Question
Find expression data from human A375 melanoma cells treated with 25uM leflunomide or DMSO for 3 days dataset (NCBI identifier: GSE24526) from NCBI’s Gene Expression Omnibus (GEO) and use it to answer the following question:
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Data is provided for ____ cancerous tissue and ____ normal bladder tissue. , (2 points each)
To save time, the relevant information from the series matrix file and the platform file have been combined and provided in the attached text file. Use this file as input to iDEP. From the DEG1 tab results, how many under-expressed (down) genes were identified?
By examining the “Gene list & data” file from DEG2 tab results, what is the gene symbol for the most under-expressed gene identified by log2 Fold Change?
From DEG2 tab results, what is the most down-regulated pathway found from GO Biological Process?
From the Pathway tab results after you select the “GSEA (preranked fgsea)” method, what is the most down-regulated pathway found from GO Biological Process?
From the Network tab results, after selecting the entire network, what was the most enriched pathway found from GO Biological Process?From a search of OMIM to find information on melanoma and dihydroorotate dehydrogenase (OMIM identifier 126064), what phenotype is associated with melanoma and dihydroorotate dehydrogenase?
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