Number of input and output field

Number of input field	:	Two
Number of output field	:	One or More

This function is used to align two deoxyribonucleic acid (DNA) or protein sequences in order to identify regions of similarity between them. These regions of similarity are useful for understanding the functional, structural, and evolutionary relationships between sequences.

Two commonly used sequence alignment algorithms are global alignment and local alignment:

Global alignment:
Global alignment compares two sequences by aligning their entire lengths and maximizing the overall similarity. This method is typically used when the sequences are similar and of approximately equal length.
Local alignment:
Local alignment focuses on aligning only the regions with the highest density of matches, rather than the entire sequence length. This approach is useful for identifying short, conserved regions within protein or nucleotide sequences.

Parameters of the SequenceAlignment Function:

Alignment Algorithm
Specifies the type of alignment to use: Global Alignment or Local Alignment.
Similarity Matrix
A similarity (substitution) matrix used to score residue similarity. Available matrices include:
DEFAULT, DNA_1, DNA_2, BLOSUM62, BLOSUM45, BLOSUM80, BLOSUM90, PAM10, PAM30, PAM70, PAM120, and PAM250
(see Substitution Matrices for more detail).

When using the DEFAULT similarity matrix, residue similarity scoring is based on the Match Score and the Mismatch Score parameters.
Match Score
The score assigned when two characters in the sequences match.
Mismatch Score
The score assigned when two characters in the sequences do not match.
Opening Gap Penalty
The penalty applied to the first gap in a gap cluster, which is the gap that immediately follows an amino acid or nucleotide in the aligned sequence.
Extension Gap Penalty
The penalty applied to each additional gap following the opening gap.
Selected Outputs
Specifies which alignment results will be forwarded to the output. Available output options include:
1. Identities(%)
2. Optimum Score
3. Total Matches
4. Total Mismatches
5. Total Opening Gaps
6. Total Extension Gaps
7. Aligned Seq 1
8. Aligned Seq 2
9. Pairwise Alignment Result
If more than one output item is selected, the results are returned in the order listed above.

Use Case : Sample of using SequenceAlignment function

Sequence 1 :

    GACCATATGATTGACGCCTATGTCAATCTCTACACTACATTGCTGGAAAGCAAATCCTGAGAGATGCTACCCCCGCCGTTGCTGCGGGGGCCAACGCGTTAATGCCGATTCTTCAGATTATCAATCACTTCTCCGAGATCCAGCCCTTGATCCTGCAACAACACCAGCAGGTGATACATCAAATCAGATGCCTCGTTGGTCAGTTCAAAGCGGTCATGTACTGTCGCTGCCAGTGCGGTTT

Sequence 2 :

    GGTKAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCYCTGGACAGATACTGACACTCAGATGCGTAAGCGTGGGGAGCAAACAGGATTAGATACCCTNGTAGTCCACGCCGTAAACGATGTCTACTTGGAGGTTGTGGCCTTNAGCCGTGGCTTTCGGACGTAACGCGTTAAGTAGACCGCCTGGGGAGTACGGTYGCAAGA

Case 1 : Parameter

    Alignment Algorithm : Global Alignment
    Similarity Matrix  : DEFAULT
    Match Score : 1
    Mismatch Score : -2
    Opening Gap Penalty : -5
    Extension Gap Penalty : -2

Results of SequneceAlignment Function :

Identities (%):

   41.05691

Optimum Score :

   -249

Total Matches :

Total Mismatches :

Total Opening Gaps :

Total Gaps :

Aligned Seq 1 :

    GACCATATGATTGACGCCTATGTCAATCTCTACACTACATTGCTGGAAAGCAAATCCTGAGAGATGCT-ACCCCC----GCCGTTGCTGCGGGGGCCAACGCGTTAATGCCGATTCTTCAGATTATCAATCACTTCTCCGAGATCCAGCCCTTGATCCTGCAACAACACCAGCAGGTGATACATCAAATCAGATGCCTCGTTGGTCAGTTCAAAGCGGTCATGTACTGTCGCTGCCAGTGCGGTTT

Aligned Seq 2 :

    GGTKAAATGCGTAGAG---ATCTGGAGGAATAC---CGGTGGCGAAGGCGGCCCYCTGGACAGATACTGACACTCAGATGCGTAAGCGTGGGGAGCAAACAGGATTA----GATAC-CCTNGTAGTCCACGCCGTAAACGATGTCTA--CTTGGAGGTTGTGGC--CTTNAGCCGTGGCT-------TTCGGACGTAACG-CGTTAAGT--AGACCGCCTGGGGAGTACGGTYGCAAGA-------

Pairwise Alignment Result:

    S1	1    GACCATATGATTGACGCCTATGTCAATCTCTACACTACATTGCTGGAAAGCAAATCCTGA 60
  	     |   | |||  |   |   || |  |    |||      | ||      |     |  ||
    S2	1    GGTKAAATGCGTAGAG---ATCTGGAGGAATAC---CGGTGGCGAAGGCGGCCCYCTGGA 54

    S1	61   GAGATGCT-ACCCCC----GCCGTTGCTGCGGGGGCCAACGCGTTAATGCCGATTCTTCA 115
  	      |||| || || | |    ||    ||   ||| || |||  | | |    ||| |  | 
    S2	55   CAGATACTGACACTCAGATGCGTAAGCGTGGGGAGCAAACAGGATTA----GATAC-CCT 109

    S1	116  GATTATCAATCACTTCTCCGAGATCCAGCCCTTGATCCTGCAACAACACCAGCAGGTGAT 175
  	       |  || |   | |   |||  || |  | | ||   ||   |  |   ||| |  | |
    S2	110  NGTAGTCCACGCCGTAAACGATGTCTA--CTTGGAGGTTGTGGC--CTTNAGCCGTGGCT 165

    S1	176  ACATCAAATCAGATGCCTCGTTGGTCAGTTCAAAGCGGTCATGTACTGTCGCTGCCAGTG 235
  	             || || |   ||  | | |||  | | ||     | | |   |  || ||  
    S2	166  -------TTCGGACGTAACG-CGTTAAGT--AGACCGCCTGGGGAGTACGGTYGCAAGA- 214

    S1	236  CGGTTT 241
  	           
    S2	215  ------ 214

Case 2 : Parameter

    Alignment Algorithm : Local Alignment
    Similarity Matrix  : DEFAULT
    Match Score : 1
    Mismatch Score : -2
    Opening Gap Penalty : -5
    Extension Gap Penalty : -2

Results of SequenceAlignment Function :

Identities (%):

   100.0