multiple choice 1. This program creates a position-specific scoring matrix (PSSM

Question

multiple choice

1. This program creates a position-specific scoring matrix (PSSM) using the top hits of a BLAST run. The PSSM is used as a substitution matrix for additional rounds of BLAST search.

a.BLAST

b.BLASTN

c.BLASTX

d.PSI-BLAST

2.You have a protein sequence and would like to search a protein sequence database for similar sequences. What specific BLAST program do you need to use?

a. BLASTP

b. BLASTN

c.BLASTX

d.TBLASTN

3.These are amino acid substitutions in homologous protein sequences that are tolerated or accepted by natural selection. They were used by Margaret Dayhoff to develop one of the first sets of amino acid substitution matrices.

a.Synonymous mutations

b.BLOCKs

c.Accepted point mutations (or point accepted mutations)

d.Identity scores

Explanation / Answer

1. D) PSI BLAST means position specific iterative basic local search tool it uses position specific scoring matrix for searching high score sequences but it give best result of high scores sequences.

2 a) BLAST P is used for searching protein sequences present in database against our protien sequence.

BLAST N is used for searching nucleotide sequence against nucleotide sequence

BLAST X is used for searching protein sequences against our nucleotide sequence (which uses 6 frames for searching )

TBLASTN used for searching nucleotide sequence ( which is y translated in 6 frames) against our protein sequence.

3 c) accepted point mutation or point accepted mutation (PAM) in this protein sequences are compared on the basis of homology. In this matrices. PAM 40 means there is less divergence while PAM 100 means more divergence

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