Please answer questions 1-4. The following is a protein sequence from the moss P
ID: 202510 • Letter: P
Question
Please answer questions 1-4.
The following is a protein sequence from the moss Physcomitrella patens XP 001758837.1 MASSSRALYLFIFSLALCHSVNAGMSNVEKIQLAFKQITTASDNLRKETQLINIINAPLQGSKIAEG 1. Please use this sequence as query and perform a regular BLAST search of NCB protein sequences a. Which BLAST program do you need to use? b. Select the "Reference proteins (Refseq_protein)" as the database. Please perform BLAST searches using "Expected threshold"10, 1, and 0.00001, respectively (you can find this option under "Algorithm parameters"). From sequences identified in each BLAST search .e., the search with a different expected threshold value), please write the species name, total score, and E value for the hit with the lowest score c. Describe the total number of hits identified using each Expected threshold value. What search provided the most hits? Which has the fewest? 2. Use the same sequence and perform a PSI-BLAST search. Use 0.00001 as Expected threshold and 3 iterations. Describe what new sequences you identified and how PSI-BLAST differs from regular BLAST searches 3. Please explain the differences between protein substitution scoring matrices and PSSM 4. Please choose the 10 most similar hits from your regular BLAST search and download their sequences in FASTA format. Now perform multiple sequence alignment using clustalo, t-coffee, and muscle, respectively. Compared your alignment results and pay attention to details, such as gaps and conserved regions. Describe the similarities and differences between results from the three alignment programs.Explanation / Answer
a. BLASTP is used in this case.
b.
Species name
Total score
E-value
Expected Threshold value
10
Physcomitrella patens
131 bits(329)
3e-37
Expected Threshold value
1
Physcomitrella patens
131 bits(329)
3e-37
Expected Threshold value
0.00001
Physcomitrella patens
131 bits(329)
3e-37
c. In all cases of expected threshold value the number of hits remains same.
2. No differences was found in case of PSI BLAST.
3. A protein substitution scoring matrix is a collection of scores for aligning amino acids with one another. These scores generally represent the relative ease with which one amino acid may mutate into or substitute for another, and they are used to measure similarity in sequence alignments. A PSSM, or Position-Specific Scoring Matrix, is a type of scoring matrix used in protein BLAST searches in which amino acid substitution scores are given separately for each position in a protein multiple sequence alignment.
Species name
Total score
E-value
Expected Threshold value
10
Physcomitrella patens
131 bits(329)
3e-37
Expected Threshold value
1
Physcomitrella patens
131 bits(329)
3e-37
Expected Threshold value
0.00001
Physcomitrella patens
131 bits(329)
3e-37