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Lab bioinformatics questions 1
Farmaceutisk cellbiologi (3FI000)
Uppsala Universitet
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Pharmaceutical cell biology Uppsala University Bioinformatics computer lab Student name:
- Sequence alignment using BLAST You are provided with a file named 'sequences', containing a sequence named 'Sequence1', extracted from a viral sample. Your task is to identify the type of virus from which this sequence originates. Visit the NCBI BLAST website at blast.ncbi.nlm.nih/Blast.cgi and choose the 'Nucleotide BLAST' option. Copy “Sequence1” from the file 'sequences' and paste this sequence into the BLAST query box and blast. Question 1A: What is the likely identity of the virus from which 'Sequence1' was derived? Now use BLAST to analyse 'Sequence 2'. Question 1B: Which human gene is most similar to this sequence?" Click on the top match, this will direct you to the 'Alignments' tab. On the right side, under the header 'Related Information' click on 'Gene – associated gene details'. Question 1C: What is the function of the gene? What Chromosome is it located on? Go back to the BLAST results. locate the 'Genome Data Viewer' under the header 'Related Information'. This will direct you to a page displaying your sequence within its genomic context. Hover over the sequence highlighted in green. A box with more information about the gene will appear. Question 1D: What is the aligned length of the sequence? How long is the protein in terms of the number of amino acids?"
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Pharmaceutical cell biology Uppsala University 2. Predict open reading frame Use the ORF Finder (ncbi.nlm.nih/orffinder/) service. Paste the nucleotide sequence of “Sequence 2” and predict the ORFs, usually the largest ORF is the most likely. Click on the coloured sequence to get a bit more information about it. Question 2A: What is an open reading frame? Question 2B: What is the start and stop of the predicted gene in your sequence? Question 2C: How many amino acids (aa) is the predicted gene? Question 2D: How do the two methods we used (BLAST and ORF finder) differ? Which method would you trust the most? 3. Searching for proteins in Uniprot Search for the human gene “Thyroid hormone receptor beta” in Uniprot (uniprot). Inspect the information that UniProt delivers. Question 3A: What is the function of the protein? Question 3B: This gene can be involved in some diseases. Give one example of a disease listed in UniProt. 4. Pairwise sequence alignment In this exercise you will align the two protein sequences “Pairwise 1” and “Pairwise 2” (available in the external document sequences) in FASTA format with the local alignment tool Water: ebi.ac/Tools/psa/emboss_water Question 4: How similar are the sequences? How many amino acids are different?
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Lab bioinformatics questions 1
Kurs: Farmaceutisk cellbiologi (3FI000)
Universitet: Uppsala Universitet
