BLAST / Blosum10 Dynamic programming gives a better alignment than BLAST. As the two sequences are very similar, it is best to use Blosum90. 12) A BLAST search is most useful when you want to do the following: Find inverted repeats within a protein sequence Generate the best possible alignment between the target and template sequences to be used as input for homology modeling Find a rat paralog to a human gene Find a rice ortholog to a yeast gene Predict the secondary structures of a protein BLAST finds similarity between sequences and does not provide the best alignment. It cannot detect inverted repeats as it is biased toward reading from left to right. Paralog are genes from the same specie. BLAST is not used for secondary structure prediction. 13) We want to find the best alignment(s) between the protein sequences FAFWC and FWFC. The scoring scheme S is defined as follows: S(i,i) = P, and S(i,j) = M otherwise. There is a constant gap penalty of G (gaps at the beginning are considered). The dynamic programming matrix is shown below. What were the values of P, M, and G: A) P=5, M=0, G=0 B) P=5, M=-1, G=-1 C) P=5, M=-2, G=-2 D) P=5, M=-3, G=-1 E) P=5, M=-1, G=-3 14) The dotplot shown below compares the DNA sequence of the actin muscle gene from Pisaster ochraceus (horizontal) with the RNA corresponding to the same gene (vertical). The six regions of high similarity that shows as black lines correspond to: 15) When we compare the sequences of proteins that belong to the same family, we observe that some regions in the sequences are more conserved than others (see for example Figure 1 below). Figure: Residues conserved among various G protein coupled receptors are highlighted in horizontal gray bars (from http://en.wikipedia.org/wiki/Conserved_sequence). The presence of such conserved regions is (choose the most likely answer):
BLAST / Blosum10 Dynamic programming gives a better alignment than BLAST. As the two sequences are very similar, it is best to use Blosum90. 12) A BLAST search is most useful when you want to do the following: Find inverted repeats within a protein sequence Generate the best possible alignment between the target and template sequences to be used as input for homology modeling Find a rat paralog to a human gene Find a rice ortholog to a yeast gene Predict the secondary structures of a protein BLAST finds similarity between sequences and does not provide the best alignment. It cannot detect inverted repeats as it is biased toward reading from left to right. Paralog are genes from the same specie. BLAST is not used for secondary structure prediction. 13) We want to find the best alignment(s) between the protein sequences FAFWC and FWFC. The scoring scheme S is defined as follows: S(i,i) = P, and S(i,j) = M otherwise. There is a constant gap penalty of G (gaps at the beginning are considered). The dynamic programming matrix is shown below. What were the values of P, M, and G: A) P=5, M=0, G=0 B) P=5, M=-1, G=-1 C) P=5, M=-2, G=-2 D) P=5, M=-3, G=-1 E) P=5, M=-1, G=-3 14) The dotplot shown below compares the DNA sequence of the actin muscle gene from Pisaster ochraceus (horizontal) with the RNA corresponding to the same gene (vertical). The six regions of high similarity that shows as black lines correspond to: 15) When we compare the sequences of proteins that belong to the same family, we observe that some regions in the sequences are more conserved than others (see for example Figure 1 below). Figure: Residues conserved among various G protein coupled receptors are highlighted in horizontal gray bars (from http://en.wikipedia.org/wiki/Conserved_sequence). The presence of such conserved regions is (choose the most likely answer):
ECS129_Final_18_solution.docx