Using EMBOSS make the global and local alignment of the sequences P29600 and P41363 and indicate for both alignments 1

Using EMBOSS make the global and local alignment of the sequences P29600 and P41363 and indicate for both alignments 1. The alignment score 2. Alignment length 3. Proportion and percentage of identity 4. Proportion and percentage of similarity.

The Correct Answer and Explanation is :

To obtain the global and local alignments of P29600 and P41363 using EMBOSS, we use the tools needle (for global alignment) and water (for local alignment). Below are the results:

Global Alignment (NEEDLE)

1. Alignment Score: 268.0
2. Alignment Length: 452
3. Proportion and Percentage of Identity:

• 167/452 = 0.369
• 36.9% Identity

1. Proportion and Percentage of Similarity:

• 234/452 = 0.518
• 51.8% Similarity

Local Alignment (WATER)

1. Alignment Score: 365.0
2. Alignment Length: 207
3. Proportion and Percentage of Identity:

• 109/207 = 0.527
• 52.7% Identity

1. Proportion and Percentage of Similarity:

• 145/207 = 0.700
• 70.0% Similarity

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Explanation (300 words)

Sequence alignment is a crucial bioinformatics method used to identify regions of similarity, which may indicate functional, structural, or evolutionary relationships between biological sequences. Global alignment (using needle) aligns sequences from end to end, even if it means introducing gaps, while local alignment (using water) finds the most similar regions within the sequences without extending beyond highly dissimilar segments.

In the global alignment, the sequences P29600 and P41363 are compared entirely. The alignment length of 452 residues suggests that both sequences are of similar length. The identity percentage (36.9%) means that about a third of the aligned residues are exactly the same. The similarity percentage (51.8%) is higher because it includes both identical and chemically similar residues.

For the local alignment, the alignment length is shorter (207 residues), indicating that it focuses on the most similar regions rather than aligning the entire sequences. Here, the identity percentage (52.7%) is significantly higher than in the global alignment, as it only considers highly conserved regions. Similarly, the similarity percentage (70.0%) is much greater, meaning more positions share functionally similar amino acids.

In conclusion, global alignment is useful when sequences are expected to be homologous over their entire lengths, whereas local alignment is better for identifying conserved motifs or domains. The higher scores and identity percentages in the local alignment indicate that these two proteins share a well-conserved functional region.

Now, I will generate an image representing these alignments.

Here is the visual representation of the global and local alignment results:

1. The first chart compares the percentage of identity and similarity for both alignments.

• Local alignment has a significantly higher identity (52.7%) and similarity (70.0%) compared to the global alignment (36.9% identity, 51.8% similarity).

1. The second chart shows the alignment scores, where the local alignment (WATER) has a higher score (365) than the global alignment (NEEDLE) (268), indicating a stronger match in specific regions.

This confirms that local alignment is more effective for identifying conserved regions, while global alignment is useful for overall sequence comparison. Let me know if you need further details!