Blastn

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

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

Which of the following is not correct about BLAST?

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

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

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

• BLAST is not based on heuristic searching methods

What is the specific format used to copy our sequence into BLAST?

• NGS

• MEGA

• SEQ

• FASTA

What is the primary purpose of the BLASTn tool in bioinformatics?

• To align protein sequences

• To align nucleotide sequences

• To predict protein structures

• To edit genetic sequences

Which of the following is a key feature of the BLASTn algorithm?

• It uses a heuristic approach

• It guarantees the optimal alignment

• It only works with protein sequences

• It requires manual sequence input

In the context of BLASTn, what does the term 'e-value' refer to?

• The number of expected hits of similar quality

• The exact match score

• The error rate of the alignment

• The energy value of the sequence

Which database is commonly used with BLASTn for nucleotide sequence alignment?

• GenBank

• PDB

• Swiss-Prot

• UniProt

What is the significance of the 'word size' parameter in BLASTn?

• It determines the length of the query sequence

• It affects the sensitivity and speed of the search

• It specifies the number of sequences to be aligned

• It sets the maximum number of mismatches allowed

How does BLASTn handle low-complexity regions in sequences?

• It ignores them completely

• It masks them to avoid spurious alignments

• It highlights them for further analysis

• It treats them as high-priority regions