EMBOSS explorer

emma

Multiple alignment program - interface to ClustalW program (read the manual)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Only produce dendrogram file?
Do alignment using an old dendrogram?
Name of old dendrogram file:
Protein align options
Select matrix
Select matrix
Filename of user pairwise matrix:
Matrix options
Select matrix
Select matrix
Filename of user multiple alignment matrix:
Additional section
Slow align options
Do you want to carry out slow or fast pairwise alignment?
Slow pairwise alignment: gap opening penalty
Slow pairwise alignment: gap extension penalty
Fast align options
Fast pairwise alignment: similarity scores: K-Tuple size (default is 1 for protein, 2 for nucleic)
Fast pairwise alignment: similarity scores: gap penalty (default is 3 for protein, 5 for nucleic)
Fast pairwise alignment: similarity scores: number of diagonals to be considered (default is 5 for protein, 4 for nucleic)
Fast pairwise alignment: similarity scores: diagonal window size (default is 5 for protein, 4 for nucleic)
Fast pairwise alignment: similarity scores: suppresses percentage score?
Gap options
Multiple alignment: Gap opening penalty
Multiple alignment: Gap extension penalty
Use end gap separation penalty?
Gap separation distance
No residue specific gaps?
List of hydrophilic residues
No hydrophilic gaps?
Cut-off to delay the alignment of the most divergent sequences
Output section
Output sequence format
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.