EMBOSS explorer

emma

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

Unshaded fields are optional and can safely be ignored. (hide optional fields)

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.