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Comparison of local and global alignment's parameters:
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- Matrix EBLOSSUM62 is used by default, it is specified by the attribute -datafile
Penalty for indel's opening -10.0. For needle it is set by -endopen, for water by -gapopen
Penalty for indel's elongation -0.5. For needle it is set by -endextend, for water by -gapextend
Penalty for the last gap is absent by default. For needle it is set by -endweight
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- There are no terminal gaps in local alignment so that allows to reach biggest percentage of conservatism and smallest percentage of gaps.
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- Comparative properties of both alignments are presented in the following table:
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| Characteristic |
Global alignment |
Local alignnment |
| Lenth |
652 |
649 |
| Totally conservative p. |
450 |
450 |
| Percentage |
69% |
69,3% |
| Functionally conservative p. |
539 |
539 |
| Percentage |
82,7% |
83,1% |
| Number of columns with gaps |
17 |
15 |
| Percentage of columns with gaps |
2,6% |
2,3% |
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Comparison of local alignment's parameters for pair homologous and five nonhomologous proteins:
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| Proteins |
Alignment's lenth |
Totally conservative |
% |
Functionally conservative |
% |
Gaps |
% |
| A0A0X8D5E1 and E8YVR4 |
52 |
10 |
19,2% |
26 |
50% |
6 |
11,5% |
| E8YVR4 and A0A109QDP9 |
24 |
8 |
33,3% |
12 |
50% |
6 |
25% |
| A0A109QDP9 and A0A1B0VIM1 |
159 |
41 |
25,8% |
57 |
35,8% |
57 |
35,8% |
| A0A1B0VIM1 and A0A0B5QAX8 |
64 |
15 |
23,4% |
28 |
43,8% |
14 |
21,9% |
| A0A0B5QAX8 and A0A0X8D5E1 |
31 |
11 |
35,5% |
13 |
41,9% |
4 |
12,9% |
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- A local alignment of nonhomologous proteins is much shorter than orignal sequences's lenth, so that means that there are a lot of terminal gaps, which were deleted by a program. Also you can see that the percentage of conservative positions is more than twice smaller and number of gaps is larger.
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Comparison of alignments built by a different programs:
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- Local alignment is shorter because of cutted down terminal parts of alignment. This is the only difference between local and global alignments
- On position 603 of plural alignment metionine corresponds to alanine when in case of global and local alignments alanine corresponds to alanine.
- On position 602 of plural alignment phenylalanine corresponds to lysine, while in global and local alignments phenylalanine corresponds to tyrosine.
- On position 617 of plural alignment glycine corresponds to alanine, while in global and local alignments it corresponds to glycine.
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- I guess that the most plausible alignment is a plural one. Residues homology is more probable because compliance is being established between few sequences.
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