Quiz1_HPB2011_2010

Which of the following is untrue regarding the gap penalty used in dynamic programming?

• Gap penalty is subtracted for each gap that has been introduced

• Gap penalty is added for each gap that has been introduced

• The gap score defines a penalty given to alignment when we have insertion or deletion

• Gap open and gap extension has been introduced when there are continuous gaps (five or more)

Which of the following does not describe dynamic programming?

• The approach compares every pair of characters in the two sequences and generates an alignment, which is the best or optimal

• Global alignment algorithm is based on this method

• A local alignment aligns a substring of the query sequence to a substring of the target sequence

• The method can be useful in aligning protein sequences to protein sequences only

Which of the following does not describe global alignment algorithm?

• In initialization step, the first row and first column are subject to gap penalty

• Score can be negative

• In trace back step, beginning is with the cell at the lower right of the matrix and it ends at top left cell

• First row and first column are set to zero

The higher is the score in the alignment, _________

• the more significant is the alignment

• the less it resembles alignments in related proteins

• the less significant is the alignment

• the less it aligns with the related protein sequence

Which of the following does not describe global alignment algorithm?

• Score can be negative in this method

• It is based on dynamic programming technique

• For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1

• For two sequences of length m and n, the matrix to be defined should be of dimensions m and n

The alignment method suitable for finding out conserved patterns in protein or DNA sequences is?

• multiple sequence alignment

• pairwise alignment

• local alignment

• global alignment