Final Exam for Bioinformatics for Biologists

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? Fill in the blank 1 of 5

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? Fill in the blank 2 of 5
• For the ORFs found when nested ORFs were ignored, how many ORFs are located on the negative strand? Fill in the blank 3 of 5
• For the ORFs found when nested ORFs were ignored, how many amino acids long is ORF17? Fill in the blank 4 of 5
• For the ORFs found when nested ORFs were ignored, what are the first 10 amino acids for the protein sequence for ORF17? Fill in the blank 5 of 5

From PSORT results, ORF17 is most commonly predicted to be a(n) ___ protein. HINT: Check the comments section for identified nearest neighbors. Fill in the blank 1 of 7
From InterPro results, what is the identifier (i.e., PF######) for the domain identified by the Pfam database? Fill in the blank 2 of 7
From Phyre2 results, what was the confidence of the ORF17 model prediction as a percentage? Fill in the blank 3 of 7
From Phyre2 results, what percent identity did the top template have for the model prediction? Fill in the blank 4 of 7
From STITCH/STRING results, which of the highest confidence proteins was found by both STITCH and STRING? Fill in the blank 5 of 7 , Fill in the blank 6 of 7 (2 points each)
What molecule weighing 665.4 g/mol was found by STITCH but not STRING? Fill in the blank 7 of 7

• What is the identity of ORF17? Fill in the blank 1 of 2
• What is the Accession number for the top BLASTP sequence identified? Fill in the blank 2 of 2

From the PROMALS3D results, how many representative sequences are there? Fill in the blank 1 of 3
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? Fill in the blank 2 of 3
From the PROMALS3D results above, how many conserved beta-strand secondary structures were predicted? Fill in the blank 3 of 3

Based on the phylogenetic tree, which species is closest species to Felis catus ORF17? Provide your answer as a NCBI locus tag. Fill in the blank 1 of 2
Based on the phylogenetic tree, which species is the furthest species from Felis catus ORF17? Provide your answer as NCBI locus tag. Fill in the blank 2 of 2

Data is provided for ____ cancerous tissue and ____ normal bladder tissue. Fill in the blank 1 of 8 , Fill in the blank 2 of 8 (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? Fill in the blank 3 of 8
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? Fill in the blank 4 of 8
From DEG2 tab results, what is the most down-regulated pathway found from GO Biological Process? Fill in the blank 5 of 8
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? Fill in the blank 6 of 8
From the Network tab results, after selecting the entire network, what was the most enriched pathway found from GO Biological Process? Fill in the blank 7 of 8

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? Fill in the blank 8 of 8