matcher

 Open help window for matcher

(Finds the best local alignments between two sequences)
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
Select an input sequence.

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:
Select an input sequence.

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:
Matrix file  
  or select a matrix file to upload here:  
  (file must contain an integer scoring matrix)
additional section
Number of alternative matches   (integer)    
Gap penalty   (Positive integer)     (default is 14 for protein, 16 for nucleic)
Gap length penalty   (Positive integer)     (default is 4 for any sequence)
output section
Alignment format:
2. Submit to matcher...
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