Bioinformatics

Which of the following statements is not correct with respect to BLAST algorithm?

• We should mask low complexity regions to speedup BLAST

• We should build indices for seed words in advance to speedup BLAST

• We should use fixed seed words inorder to speedup BLAST

• We should use shorter seed words inorder to speedup BLAST

Which of the following statements is not correct with respect to BLAST algorithm?

• We should mask low complexity regions to speedup BLAST

• We should use dynamic programming at the first stage to speedup BLAST

• We should build indices for seed words in advance to speedup BLAST

• We should use longer seed words inorder to speedup BLAST

BLAST uses dynamic programming in the last step to produce gapped alignment

• TRUE

• FALSE

Why does BLAST use dynamic programming to realign the sequence after extending the hit cluster?

• To find optimum alignment of query around hit cluster

• To calculate directly the p-value probability that this alignment is by random chance

• There is no reason, and this step is optional

A= Compares an amino acid query sequence against a protein sequence database

B= Compares a nucleotide query sequence against a nucleotide sequence database

• A= BLASTN B=BLASTP

• A=BLASTP, B=BLASTN

• A= BLASTX B=BLASTN

• A=TBLASTN B=BLASTX

Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames

• BLASTX

• BLASTP

• TBLASTN

• TBLASTX

The BLAST program was developed in _______

• a) 1992

• b) 1995

• c) 1990

• d) 1991

A recent improvement in the implementation of BLAST is the ability to provide gapped alignment.

• a) True

• b) False

In sequence alignment by BLAST, each word from query sequence is typically _______ residues for protein sequences and _______ residues for DNA sequences.

• a) ten, eleven

• b) three, three

• c) three, eleven

• d) three, ten

Which of the following is not correct about BLAST?

• a) The BLAST web server has been designed in such away as to simplify the task of program selection

• b) The programs are organized based on the type of query sequences

• c) The programs are organized based on the type of nucleotide sequences, or nucleotide sequence to be translated

• d) BLAST is not based on heuristic searching methods