Command - displays command (needle - global alignment, water - local alignment);
Aligned length - displays length of alignment;
Indels - displays number of indels - parts of sequence, where insertion or the deletion of bases must have happened^[1];
Gaps - dispays number of gaps (group of gaps = indel);
Identity - displays the required number of identities at a position for it to give a consensus;
Similarity - displays a cut-off for the % of positive scoring matches below which there is no consensus.

1. • Jalview pairwise needle sequence alignment (link)
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   Figure 1. Screenshot of part of the needle alignment
   
   
2. • Jalview pairwise water sequence alignment (link)
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Figure 2. Screenshot of part of the water alignment

Table 3. Default data for needle and water EMBOSS commands

	Needle	Water
Matrix (for protein sequences)	EBLOSUM62	EBLOSUM62
Gap open penalty	10.0 (endopen)	10.0 (gapopen)
Gap length penalty	0.5 (endextend)	0.5 (gapextend)
Gap end penalty	- (endweight)	-

Differences^[2]

Global Sequence Alignment (Needle)	Local Sequence Alignment (Water)
In global alignment, an attempt is made to align the entire sequence (that's why there are more gaps).	Finds local regions with the highest level of similarity between the two sequences (that's why the start of sequences is cut off).
A global alignment contains all letters from both the query and target sequences	A local alignment aligns a substring of the query sequence to a substring of the target sequence.
If two sequences have approximately the same length and are quite similar, they are suitable for global alignment (more suitable for aligning two homological sequences).	Any two sequences can be locally aligned as local alignment finds stretches of sequences with high level of matches without considering the alignment of rest of the sequence regions (suitable for aligning more divergent sequences or distantly related sequences).
A global alignment technique is the Needleman–Wunsch algorithm.	A local alignment method is Smith–Waterman algorithm.

Task 2

Used programs: EMBOSS, Jalview
EMBOSS commands: needle, water
Steps: Input Alignment - From File - file.fasta - Colour - ClustalX - Above Identity Threshold (100%)

Table 4. Water sequence alignment of non-homological sequences (proteins with different functions were taken). All 5 sequences were aligned with my protein, BAC73082.1.

Protein	Aligned Length	Gaps	Indels	% (Indels)	Identity	% (Identity)	Similarity	%(Similarity)
AKC28878.1	32	0/0	0/0	0/0	32/8	100.0/25.0	0/8	0/25.0
AMM47000.1	39	2/0	5/0	12.8/0	34/16	87.2/41.0	0/7	0/17.9
AFH91095.1	140	4/3	26/30	18.6/21.4	114/53	81.4/37.9	0/18	0/12.9
AMD46139.1	53	2/1	6/1	11.3/1.9	47/19	88.7/35.8	0/10	0/18.9
AJG99379.1	67	1/3	2/21	3.0/3.1	65/20	97.0/29.9	0/7	0/10.4

Differences between homological protein alignment and non-homological protein alignment

The main difference which i was able to spot is the length of alignment. It's way shorter than the homological alignment (seems logical to me).

Task 3

Figure 3. Screenshot of part of the alignment (from top to bottom: TCoffee Multiple - Needle Pairwise - Water Pairwise)

• Jalview alignment (link)
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Mismatches

1. Length - Needle and Water alignments are much shorter and Water alignment has no first part (starts from M residue);
2. Multiple alignment has more gaps than the others; I suppose there should be gaps as TCoffee aligned more sequences;
3. GLY: 37 position in TCoffee, 8 position in Needle, 2 position in Water.

I think that the TCoffee Multiple Aligning Service is the best choice. It aligned two sequences more accurately as it 'compared' more sequences so it must has taken all indels into account.

References

1. Wikipedia Indel page.
2. Differences between local and global sequence alignment.

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© Sophia Veselova, 2017.