Biology: Bioinformatics: Reading DNA Sequence Alignments
Interpreting matches, mismatches, gaps, and conserved DNA regions
Biology: Bioinformatics: Reading DNA Sequence Alignments
Interpreting matches, mismatches, gaps, and conserved DNA regions
Biology - Grade 9-12
- 1
In the alignment below, identify the positions where the two DNA sequences are different. Sequence A: ATGCCGTAA Sequence B: ATGTCGTGA
Compare the sequences one position at a time from left to right.
The sequences are different at positions 4 and 8. At position 4, Sequence A has C and Sequence B has T. At position 8, Sequence A has A and Sequence B has G. - 2
Calculate the percent identity for these aligned sequences. Sequence A: ATGCCGTAA Sequence B: ATGTCGTGA
The percent identity is 7 matches out of 9 total aligned positions, which is 7 divided by 9 times 100. The percent identity is about 77.8%. - 3
In the alignment below, a dash represents a gap. What type of mutation does the gap most likely represent in Sequence B compared with Sequence A? Sequence A: ATGCAAGT Sequence B: ATG-AAGT
A missing nucleotide in one sequence is shown as a dash in the alignment.
The gap most likely represents a deletion in Sequence B compared with Sequence A. Sequence B is missing the C found at position 4 in Sequence A. - 4
Use the alignment to count the number of matches, mismatches, and gaps. Sequence A: A T G C A T G C Sequence B: A T - C G T G A
There are 5 matches, 2 mismatches, and 1 gap. The matches are at positions 1, 2, 4, 6, and 7. The mismatches are at positions 5 and 8, and the gap is at position 3. - 5
The symbol line below uses a vertical bar to mark identical bases. Explain what the alignment shows. Sequence A: ATGCCATT Symbol line: ||| ||| Sequence B: ATGACATG
A vertical bar means the bases above and below that position are the same.
The alignment shows that the two sequences match at positions 1, 2, 3, 5, 6, and 7. They differ at positions 4 and 8, where the bases are not identical. - 6
Which part of this alignment appears most conserved across all three species? Human: ATGCTACCGT Chimpanzee: ATGCTACCGT Mouse: ATGCTATCGT
Positions 1 through 6 and positions 8 through 10 appear conserved across all three species. Position 7 is different because the mouse sequence has T while the human and chimpanzee sequences have C. - 7
Based on this alignment, which two species have the most similar DNA sequence? Explain your answer. Species 1: AATGCCGA Species 2: AATGCTGA Species 3: TATACCAA
Count how many positions differ between each pair of species.
Species 1 and Species 2 have the most similar DNA sequences. They differ at only one position, while each is more different from Species 3. - 8
A student says, 'Two sequences with 100% identity must come from the same species.' Explain why this statement is not always correct.
The statement is not always correct because different species can share identical DNA sequences in conserved genes or short regions. A 100% match in one region does not prove that two organisms are the same species. - 9
Look at the alignment below. Does the mutation at position 6 appear to be a substitution, insertion, or deletion? Reference: ATGCCAAT Sample: ATGCCGAT
A substitution changes one nucleotide to another without adding or removing a position.
The mutation at position 6 is a substitution. The reference has A at position 6, while the sample has G at the same aligned position. - 10
A DNA alignment has 48 identical positions out of 60 total aligned positions. Calculate the percent identity.
The percent identity is 48 divided by 60 times 100. This equals 80%, so the two sequences have 80% identity. - 11
In a coding DNA sequence, an insertion or deletion of 1 nucleotide can cause a frameshift. Explain why a single nucleotide gap in an alignment may be important.
Codons are read in groups of three nucleotides.
A single nucleotide gap may be important because it can shift the reading frame of a coding sequence. This can change many amino acids after the mutation and may strongly affect the protein. - 12
Use the alignment to identify the consensus base at each position. The consensus base is the base that appears most often in that column. Seq 1: A T G C A Seq 2: A T G T A Seq 3: A C G C A Seq 4: A T G C G
The consensus sequence is ATGCA. Position 1 is A, position 2 is T, position 3 is G, position 4 is C, and position 5 is A because each is the most common base in its column. - 13
A researcher aligns the same gene from four bacteria and finds that one region is nearly identical in all four bacteria. What might this suggest about that region?
Conserved regions often change slowly because they are important.
This may suggest that the region is conserved because it has an important function. Mutations in that region may be harmful, so natural selection may preserve the sequence over time. - 14
Read the alignment and identify the single nucleotide polymorphism, or SNP, position. Reference: G C T A A C T Sample 1: G C T A A C T Sample 2: G C T G A C T Sample 3: G C T A A C T
The SNP is at position 4. Most sequences have A at position 4, but Sample 2 has G at that position. - 15
Two students compare DNA alignments. Alignment A is 20 bases long with 18 matches. Alignment B is 200 bases long with 160 matches. Which alignment has the higher percent identity, and why?
Percent identity depends on the fraction of matching positions, not just the number of matches.
Alignment A has the higher percent identity. Alignment A is 18 divided by 20 times 100, which is 90%. Alignment B is 160 divided by 200 times 100, which is 80%.