BI

The procedure of aligning 2 sequences by searching for pattern that is in the same order in the sequences.

• Sequence alignment

• Pairwise alignment

• Multiple sequence alignment

• All of these

Alignment method suitable for aligning closely related sequence is

• Multiple sequence alignment

• Pairwise sequence alignment

• Global alignment

• Local alignment

When did Smith–Waterman first describe the algorithm for local alignment?

• 1955

• 1970

• 1981

• 1925

Which of the following does not describe local alignment?

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

• A local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score

• Local alignment have terminal gaps

• The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global

Local alignments are more used when _____________.

• There are totally similar and equal length sequences

• Dissimilar sequences are suspected to contain regions of similarity

• Similar sequence motif with larger sequence context

• Partially similar, different length and conserved region containing sequences

Which of the following does not describe BLOSUM matrices?

• It stands for BLOcks SUbstitution Matrix

• It was developed by Henikoff and Henikoff

• The year it was developed was 1992

• These matrices are logarithmic identity values

Among the following which one is not the approach to the local alignment?

• Smith-Waterman algorithm

• K-tuple method

• Words method

• Needleman-Wunsch algorithm

Which of the following does not describe BLAST?

• It stands for Basic Local Alignment Search Tool

• It uses word matching like FASTA

• It is one of the tools of the NCBI

• Even if no words are similar, there is an alignment to be considered

Which of the following is untrue regarding BLAST and FASTA?

• FASTA is faster than BLAST

• FASTA is the most accurate

• BLAST has limited choices of databases

• FASTA is more sensitive for DNA-DNA comparisons

Which of the following does not describe local alignment algorithm?

• Score can be negative

• Negative score is set to 0

• First row and first column are set to 0 in initialization step

• In traceback step, beginning is with the highest score, it ends when 0 is encountered