emma

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(Multiple alignment program - interface to ClustalW program)
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1. Set the parameters for the run (or accept the defaults...)
input section
Select a set of sequences.

Use one of the following three fields:  

  1. To access a sequence from a database, enter the USA path here: (dbname:entry)

  2. Or, upload a sequence file from your local computer here:

  3. Or enter the sequence data manually here:
Error
unknown datatype 'toggle'
Error
unknown datatype 'toggle'
Dendrogram (tree file) from clustalw file (optional)  
 
protalignsection section
Select matrix
Select matrix
Comparison matrix file (optional)  
 
matrixsection section
Select matrix
Select matrix
Comparison matrix file (optional)'  
 
additional section
slowalignsection section
Error
unknown datatype 'toggle'
Slow pairwise alignment: gap opening penalty   (real number)    
Slow pairwise alignment: gap extension penalty   (real number)    
fastalignsection section
Fast pairwise alignment: similarity scores: K-Tuple size   (integer from 0 to 4)     (default is 1 for protein, 2 for nucleic)
Fast pairwise alignment: similarity scores: gap penalty   (Positive integer)     (default is 3 for protein, 5 for nucleic)
Fast pairwise alignment: similarity scores: number of diagonals to be considered   (Positive integer)     (default is 5 for protein, 4 for nucleic)
Fast pairwise alignment: similarity scores: diagonal window size   (Positive integer)     (default is 5 for protein, 4 for nucleic)
Fast pairwise alignment: similarity scores: suppresses percentage score?  
gapoptions section
Multiple alignment: Gap opening penalty   (Positive foating point number)    
Multiple alignment: Gap extension penalty   (Positive foating point number)    
Use end gap separation penalty?  
Gap separation distance   (Positive integer)    
No residue specific gaps?  
List of hydrophilic residues  
 
No hydrophilic gaps?  
Cut-off to delay the alignment of the most divergent sequences   (Integer from 0 to 100)    
output section
Output file format:
Dendrogram (tree file) from clustalw output file  
2. Submit to emma...
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