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BIO5INF: Nucleotide - SMART Criteria - Bioinformatics Assignment Help
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28. Victor treated cancer cells with and without a chemotherapeutic drug doxorubicin. He obtained the results for 24 and 48 hours after treatment with or without the drug. While analysing the data, he is unsure of what parameters he should use to calculate the significance by T-test? Can you select the right parameters he should use?
29. While using SMART for domain analysis, if you choose “Normal SMART”, what databases will be present?
Task: 2
Please put the answers to these questions into a MS Word file in landscape format and submit into the Assignment inbox on LMS called ‘Bioinformatics Exam Section 3 Submission’ which can be found under the ‘Bioinformatics Assessments’ tab. This submission inbox will be unavailable after the test.
Take a screenshot of the molecule along with the ‘graphical representations’ box showing. Adjust the width of the box to ensure that all details of your selections are visible.
2. An antibody has been raised against the following protein:
i. What is the name of the protein? You need to determine the subcellular localisation of this protein when the antibody is tested on the animal tissue. However, the sequence provided is not inclusive of the signal sequence. ii. Describe how you would solve this problem using any Bioinformatics tools you wish. Attach relevant screenshots to aid your explanation.
2. Hector works on a mouse protein with accession NP_033268.1. During his seminar, a colleague questioned him about the percentage of homology and identity of this accession ID with rat.
i. What is the percentage of homology and identity of NP_033268.1 with similar protein in rat (NP_036788.1)?
ii. Describe how you would solve this problem using any Bioinformatics tools you wish. Attach relevant screenshots to aid your explanation.
Task: 3
Use the following accession number to answer these questions: NP_003109.1
1. a.What is the name of the transcript/mRNA?
b. What is the name of the protein?
c. On what chromosome is it located?
d. What is its Gene ID?
2. How many isoforms are there for gene the codes this protein?
3. How many nucleotides in the mRNA?
4. a) How many exons are in this nucleotide?
b) How many exons code for amino acids in this nucleotide?
5. a) According to PSORT II’s MITDISC, what is the D/E content for the protein?
b) Using SMART domain tool, can you predict the most likely subcellular localization of this protein? Reason why.
6. How many possible TM helices are there in this protein? What program did you use to find this information?
7. a) Using NR protein database, what protein in cow has the highest homology to your protein? Enter the RefSeq ID of the protein.
b) What is the organism of the highest homologous protein and also mention the ‘Max score’ for this alignment?
8. a) Using SMART (without selecting outlier homologues, PFAM domains, signal peptides and internal repeats), what domains are present in this protein
b) Using SMART, name one more protein in Homo sapiens that has the FOLN domain?
c) Using SMART, what percentage of proteins containing the domain FOLN are involved in TGF-beta signaling pathway?
9. a) Does the protein have a signal peptide using SignalP?
b) If so, can you tell the amino acids position for signal peptide?
c) If so, between which amino acids does the cleavage happen?
d) What is the mean S-score ‘Value’?
Task: 4
You are given a plasmid (a circular piece of DNA) that contains a sequence coding for a human anti-apoptotic protein (i.e. a protein that stops cell death). You transfect it into some mammalian cells in a dish and also add some doxorubicin (a drug that causes cell death). You repeat this ten times. After 24 hr, you look for cell death, and get the following results.
1. a) For cells transfected with plasmid, what is the SD
b) For cells not transfected with plasmid, what is the SD?
c) For cells transfected with plasmid, what is the mode?
d) For cells not transfected with plasmid, what is the mode?
2. a) What is the pI of the protein encoded by NM_003118.3 as per ProtParam tool?
b) What is the total number of negatively charged residues?
c) What is GRAVY score for the precursor and mature protein (after signal peptide is cleaved)?
3. How many protein isoforms are available for the Entrez Gene ID: 2195 or gene symbol FAT1? How many predicted and reviewed/validated?
4. If you have 9 amino acid peptide, what will be the approximate molecular weight in kDa?
5. Mention what is wrong with the fasta format protein sequence below. The protein is only localized in nucleus.
gi|Me protein or mRNA?|NP_12345.1
BCDEFGHBMPEETVAEVTEVSVGANPVQVEVGEFDDGAASTY
Task: 5
Please put the answers to these questions into a MS Word file in landscape format and submit into the Assignment inbox on LMS called ‘Bioinformatics Exam Section 3 Submission’ which can be found under the ‘Bioinformatics Assessments’ tab. This submission inbox will be unavailable after 11:30 am.
Take a screenshot of the molecule along with the ‘graphical representations’ box showing. Adjust the width of the box to ensure that all details of your selections are visible.
2. An antibody has been raised against the following protein (sequence in LMS – Ab-Seq):
3. What is the name of the protein? You need to determine the subcellular localisation of this protein when the antibody is tested on the animal tissue. However, the sequence provided is not inclusive of the signal sequence.
4. Describe how you would solve this problem using any Bioinformatics tools you wish. Attach relevant screenshots to aid your explanation.
Bioinformatics Assignment Help
Task: 1 1. What is the name of the transcript/mRNA with the RefSeq Accession NP_003109.1? 2. How many isoforms are there for NCBI Entrez Gene ID: 1956? 3. How many exons are there for NCBI Entrez Gene ID: 13649? 4. In NM_0031183.3, how many exons code for the protein? 5. According to PSORT II’s MITDISC, what is the D/E content for UniProt accession P98160? 6. Using SMART domain tool, can you predict the most likely subcellular localization of the protein P98160? Reason why. 7. How many possible TM helices are there in this protein P98160? What program did you use to find this information? 8. Using RefSeq protein database, what protein in human has the highest homology to your protein P01137? Enter the RefSeq ID of the protein. 9. Michael needs to find more about the Accession ID NM_2349801.23. As a start, what molecule type is he interested in? 10. Using SMART (without selecting outlier homologues, PFAM domains, signal peptides and internal repeats), what domains are present in the protein NP_000592.3? 11. Using SMART, name one protein in Homo sapiens that has the SH2 domain? 12. Ken intends to predict mitochondrial targeting sequence using PSORT II. From the results page, what subprogram will he look into? 13. Using SMART, what percentage of proteins containing the domain FOLN are involved in TGF-beta signaling pathway? 14. Does the protein NP_001121363.1 have a signal peptide by using SignalP? 15. Can you tell the amino acid position for signal peptide in the protein NP_001121363.1 (if present)? (e.g., 304-315 or not present) 16. Between which amino acids does the cleavage happen for the signal peptide in the protein NP_001121363.1? (e.g., 98-99; P-L or not present) 17. What is the mean S-score ‘Value’ for the protein NP_001121363.1 using SignalP? 18. What is the pI of the protein encoded by NM_003118.3 as per ProtParam tool? 19. What is the total number of negatively charged residues for NP_001121363.1 as per ProtParam tool? 20. What is GRAVY score for the precursor and mature protein NP_001296372.1 (after signal peptide is cleaved)? 21. How many protein isoforms are available for the Entrez Gene ID: 2195 or gene symbol FAT1? How many predicted and reviewed/validated? 22. Mention what is wrong with the fasta format protein sequence below. The protein is only localized in nucleus. gi|Me protein or mRNA?|NP_12345.1 BCDEFGHBMPEETVAEVTEVSVGANPVQVEVGEFDDGAASTY 23. A signal peptide is predicted to be present in a protein of interest? Select the likely position of the signal peptide in the protein sequence. 24. If you have a 7 amino acid peptide sequence, what will be the approximate molecular weight? 25. If you have to find a similar protein for the following sequence, which BLAST will you use? 26. One of the cell donated by a male human had 23 pairs of chromosomes. Given that he has only one Y chromosome, how many reading frames will need to be considered while predicting genes in Y chromosome? 27. TMHMM results for a protein of interest is given below. Based on the results, select the correct topology?
28. Victor treated cancer cells with and without a chemotherapeutic drug doxorubicin. He obtained the results for 24 and 48 hours after treatment with or without the drug. While analysing the data, he is unsure of what parameters he should use to calculate the significance by T-test? Can you select the right parameters he should use?
29. While using SMART for domain analysis, if you choose “Normal SMART”, what databases will be present?
Task: 2
Please put the answers to these questions into a MS Word file in landscape format and submit into the Assignment inbox on LMS called ‘Bioinformatics Exam Section 3 Submission’ which can be found under the ‘Bioinformatics Assessments’ tab. This submission inbox will be unavailable after the test.
- Open the molecule 5XF3 in VMD. Manipulate the molecule to show the following:
- DNA in ‘ribbons’ rendering in purple
- Histone H4 in ‘surf’ rendering in yellow
- Ruthenium in ‘quicksurf’ rendering in red
- Sulphur in ‘beads’ rendering in white
- Rotate your molecule so that it matches the axis as below:
Take a screenshot of the molecule along with the ‘graphical representations’ box showing. Adjust the width of the box to ensure that all details of your selections are visible.
2. An antibody has been raised against the following protein:
i. What is the name of the protein? You need to determine the subcellular localisation of this protein when the antibody is tested on the animal tissue. However, the sequence provided is not inclusive of the signal sequence. ii. Describe how you would solve this problem using any Bioinformatics tools you wish. Attach relevant screenshots to aid your explanation.
2. Hector works on a mouse protein with accession NP_033268.1. During his seminar, a colleague questioned him about the percentage of homology and identity of this accession ID with rat.
i. What is the percentage of homology and identity of NP_033268.1 with similar protein in rat (NP_036788.1)?
ii. Describe how you would solve this problem using any Bioinformatics tools you wish. Attach relevant screenshots to aid your explanation.
Task: 3
Use the following accession number to answer these questions: NP_003109.1
1. a.What is the name of the transcript/mRNA?
b. What is the name of the protein?
c. On what chromosome is it located?
d. What is its Gene ID?
2. How many isoforms are there for gene the codes this protein?
3. How many nucleotides in the mRNA?
4. a) How many exons are in this nucleotide?
b) How many exons code for amino acids in this nucleotide?
5. a) According to PSORT II’s MITDISC, what is the D/E content for the protein?
b) Using SMART domain tool, can you predict the most likely subcellular localization of this protein? Reason why.
6. How many possible TM helices are there in this protein? What program did you use to find this information?
7. a) Using NR protein database, what protein in cow has the highest homology to your protein? Enter the RefSeq ID of the protein.
b) What is the organism of the highest homologous protein and also mention the ‘Max score’ for this alignment?
8. a) Using SMART (without selecting outlier homologues, PFAM domains, signal peptides and internal repeats), what domains are present in this protein
b) Using SMART, name one more protein in Homo sapiens that has the FOLN domain?
c) Using SMART, what percentage of proteins containing the domain FOLN are involved in TGF-beta signaling pathway?
9. a) Does the protein have a signal peptide using SignalP?
b) If so, can you tell the amino acids position for signal peptide?
c) If so, between which amino acids does the cleavage happen?
d) What is the mean S-score ‘Value’?
Task: 4
You are given a plasmid (a circular piece of DNA) that contains a sequence coding for a human anti-apoptotic protein (i.e. a protein that stops cell death). You transfect it into some mammalian cells in a dish and also add some doxorubicin (a drug that causes cell death). You repeat this ten times. After 24 hr, you look for cell death, and get the following results.
1. a) For cells transfected with plasmid, what is the SD
b) For cells not transfected with plasmid, what is the SD?
c) For cells transfected with plasmid, what is the mode?
d) For cells not transfected with plasmid, what is the mode?
2. a) What is the pI of the protein encoded by NM_003118.3 as per ProtParam tool?
b) What is the total number of negatively charged residues?
c) What is GRAVY score for the precursor and mature protein (after signal peptide is cleaved)?
3. How many protein isoforms are available for the Entrez Gene ID: 2195 or gene symbol FAT1? How many predicted and reviewed/validated?
4. If you have 9 amino acid peptide, what will be the approximate molecular weight in kDa?
5. Mention what is wrong with the fasta format protein sequence below. The protein is only localized in nucleus.
gi|Me protein or mRNA?|NP_12345.1
BCDEFGHBMPEETVAEVTEVSVGANPVQVEVGEFDDGAASTY
Task: 5
Please put the answers to these questions into a MS Word file in landscape format and submit into the Assignment inbox on LMS called ‘Bioinformatics Exam Section 3 Submission’ which can be found under the ‘Bioinformatics Assessments’ tab. This submission inbox will be unavailable after 11:30 am.
- Open the molecule 5HU6 in VMD. Manipulate the molecule to show the following:
- Haptoglobin in ‘surf’ rendering in white
- Haemoglobin Receptor in ‘new cartoon’ rendering in red
- Haemoglobin in ‘lines’ rendering in yellow
- All metal ions in ‘quicksurf’ rendering in purple.
- Rotate your molecule so that it matches the axis as below:
Take a screenshot of the molecule along with the ‘graphical representations’ box showing. Adjust the width of the box to ensure that all details of your selections are visible.
2. An antibody has been raised against the following protein (sequence in LMS – Ab-Seq):
3. What is the name of the protein? You need to determine the subcellular localisation of this protein when the antibody is tested on the animal tissue. However, the sequence provided is not inclusive of the signal sequence.
4. Describe how you would solve this problem using any Bioinformatics tools you wish. Attach relevant screenshots to aid your explanation.
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