Determine whether each statement is True or False 1.BLOSUM substitution matrices

Question

Determine whether each statement is True or False

1.BLOSUM substitution matrices are derived from amino acid changes observed in multiply aligned sequences found in motifs and domains.

2.The default substitution scoring matrix for BLASTP in NCBI is PAM100.

3.A progressive multiple sequence alignment program uses a phylogenetic tree to guide the order of sequence addition and final alignment.

4.The higher the similarity score for a hit in BLAST search, the lower the E-value.

5. The similarity score (or alignment score) for two pairwise aligned sequences are always the same no matter what amino acid substitution scoring matrix is used.

Explanation / Answer

1. True.

2. False.
BLOSUM62 is the default matrix for BLASTP.

3. True.
Progressive alignment methods occurs in two stages: 1. The relationships between the seq. are represented as a guide tree, and 2. MSA is built by adding the seq. sequentially to the growing MSA according to the guide tree.

4. True.
E value essentially describes the random background noise, the lower the value is, the more "significant" the match is.

5. False.

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