Number of input and output field

Number of input field	:	One
Number of output field	:	One Or More

This transformation function is used to generate the alignment of three or more biological sequences (protein or nucleic acid) of similar length using the Progressive Alignment Method.

Parameters of the MultipleSequenceAlignment Function

• Sequences Separator
  The character used to separate individual sequences in the input.
• 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 the DEFAULT similarity matrix is used, residue similarity scoring is based on the Match Score and the Mismatch Score parameters.
• Match Score
  The score assigned for a match between two characters in the sequences.
• Mismatch Score
  The score assigned for a mismatch between two characters in the sequences.
• 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 results of the multiple sequence alignment will be forwarded to the output. Available options include:
  
  1. Similarity
  2. Score
  3. Alignments
  If the number of selected output information items is more than one, then the order is according to the ordering mentioned above.

---

Use Case: A Sample of Using the MultipleSequenceAlignment Function

Sequences input :

    QPVHPFSRPAPVVIILIILCVMAGVIGTILLISYGIRLLIK
    QLVHRFTVPAPVVIILIILCVMAGIIGTILLISYTIRRLIK
    QLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKSPSDVKPLPSPD
    QLVHEFSELVIALIIFGVMAGVIGTILFISYGSRRLIKKSESDVQPLPPPD
    MLEHEFSAPVAILIILGVMAGIIGIILLISYSIGQIIKKRSVDIQPPEDED
    PIQHDFPALVMILIILGVMAGIIGTILLISYCISRMTKKSSVDIQSPEGGD
    QLVHIFSEPVIIGIIYAVMLGIIITILSIAFCIGQLTKKSSLPAQVASPED
    LAHDFSQPVITVIILGVMAGIIGIILLLAYVSRRLRKRPPADVP
    SYHQDFSHAEITGIIFAVMAGLLLIIFLIAYLIRRMIKKPLPVPKPQDSPD

The Parameters :

    Sequences Separator : \n
    Similarity Matrix  : BLOSUM62
    Match Score : 1
    Mismatch Score : -2
    Opening Gap Penalty : -5
    Extension Gap Penalty : -2

Results of the MultipleSequenceAlignment Function:

Similarity :

   0.4368317825214376

Score :

   2757.0

Alignments:

    S1    1   QPVH-PFSRPAPVVIILIILCVMAGVIGTILLISYGIRLL----------------IK 41
    S2    1   QLVH-RFTVPAPVVIILIILCVMAGIIGTILLISYTIRRL----------------IK 41
    S3    1   QLAH-HFS--EPEI-TLIIFGVMAGVIGTILLISYGIRRLIKKSPSDVKPLPSP---D 51
    S4    1   QLVH-EFS--ELVI-ALIIFGVMAGVIGTILFISYGSRRLIKKSESDVQPLPPP---D 51
    S5    1   MLEH-EF--SAPVA-ILIILGVMAGIIGIILLISYSIGQIIKKRSVDIQ---PPEDED 51
    S6    1   PIQH-DF--PALVM-ILIILGVMAGIIGTILLISYCISRMTKKSSVDIQ---SPEGGD 51
    S7    1   QLVH-IFS--EPVI-IGIIYAVMLGIIITILSIAFCIGQLTKKS-SLPAQVASPE--D 51
    S8    1   -LAH-DFSQ--PVITV-IILGVMAGIIGIILLLAYVSRRLR-KR--------PPADVP 44
    S9    1   -SYHQDFS--HAEI-TGIIFAVMAGLLLIIFLIAYLIRRMIKKPLPVPKPQDSP---D 51
              .. *  *.   ..: . **: **:*::..*::::: ...: .:         .:   .