Question

What are pairwise alignments used for?
(Mark all correct answers. Multiple answers possible.)

	1.	Pairwise alignments are used in DotPlots.
	2.	Pairwise alignments can be used to create consensus sequences.
	3.	Scores from pairwise alignments are sometimes used in Multiple Sequence Alignments, MSAs, to determine relatedness in preparing assembly trees.
	4.	Pairwise alignments are used to refine some alignments within some Multiple Sequence Alignments, MSAs.
	5.	Pairwise alignments are used to compare two sequences either in local alignments (conserved regions) or over the length of the two sequences in global alignments.
	6.	Pairwise alignments are used to define Single Nucleotide Polymorphisms, SNPs.
	7.	The scores from pairwise alignments between a sequence and it's shuffled mate are used to develop distributions designed to determine the significance of the alignment between the sequence and it's un-shuffled mate.
	8.	Pairwise alignments are used to define conserved domains between two sequences.

Answer 1

1. To observe the similar properties of protein and nucleic acid sequences are used for similar matrix is said to be dot plot.

Therefore, in pairwise alignments the dot plots are used.

2. Consensus sequence are used in determining the alignment of many nucleotide or protein sequence share the common functions then commonly expressed nucleotide that is amino acid are determined in every position.

Therefore option 2 is incorrect.

3.Multiple sequence alignment are used in pairwise alignments sequence to mostly to implement the sequence more than two sequences at once.

Therefore, this option is correct.

4.Protein sequence alignment are used to refining or to know the accuracy in alignment.

This makes the option (4) incorrect.

5. Global alignment include each letter including both target and query sequence. End to end alignment.

Local alignment align the substring the query sequence to the substring the Target sequence.

To determine alignment between two sequences. these both are used during pairwise alignments.

This makes the option 5 correct.

6.Single nucleotide polymorphisms are used to determine the substitution of a nucleotide which occur on the specific position in genomes.

This makes the option 6 incorrect.

7. Ushuffle sequence are the sequence mostly used in the matrix tree theorem. and to generate random permutation in uniformed manner of the biological sequence such as protein RNA and DNA.

This makes the option 7 incorrect.

8. Conserved domain are used multiple sequence alignment hence it represent the two different databaseprotein sequence and the amino acid sequence with similar pattern.

This makes the option 8 incorrect.