water

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(Smith-Waterman local 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
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 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:
required section
Gap opening penalty   (real number)     (default is 10.0 for any sequence)
Gap extension penalty   (real number)     (default is 0.5 for any sequence)
advanced section
Matrix file  
  or select a matrix file to upload here:  
  (file must contain a floating point scoring matrix)
output section
Brief identity and similarity?  
Alignment format:
2. Submit to water...
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