Open help window for showalign

(Displays a multiple sequence alignment)

Fields with a coloured background are optional and can safely be ignored...
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1. Set the parameters for the run (or accept the defaults...)
input section
The sequence alignment to be displayed..

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:

Similarity scoring Matrix file  
  or select a matrix file to upload here:  
  (file must contain an integer scoring matrix)
additional section
The number or the name of the reference sequence  
Display the reference sequence at the bottom?  
What to show
Output order of the sequences
Show similar residues in lower-case?  
Display the consensus line?  
advanced section
Regions to put in uppercase (eg: 4-57,78-94)  
  (If this is left blank, then the sequence case is left alone.)
Number the sequences?  
Display ruler?  
Width of sequence to display   (integer)    
Length of margin for sequence names   (integer)    
Use HTML formatting?  
Regions to colour in HTML (eg: 4-57 red 78-94 green)  
Plurality check % for consensus   (real number)    
Threshold above which the consensus is given in uppercase   (real number)    
Required % of identities at a position for consensus   (real number)    
Use gap characters in consensus?  
output section
Output file name  
2. Submit to showalign...
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