EMBOSS explorer

prettyplot

Draw a sequence alignment with pretty formatting (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:

Matrix file. Use one of the following two fields:

  1. To access a standard EMBOSS data file, enter the name here: (default is EBLOSUM62 for protein, EDNAFULL for nucleic)
  2. To upload a data file from your local computer, select it here:
Additional section
Number of residues to be displayed on each line
Residues before a space (default is Same as -residuesperline to give no breaks)
Colour residues by their consensus value.?
Colour to display identical residues (RED)
Colour to display similar residues (GREEN)
Colour to display other residues (BLACK)
Colour residues by table oily, amide etc.?
Shading
Values to represent identical similar related
Only match those which are identical in all sequences.
Display prettyboxes?
Colour the background in the boxes?
Colour to be used for background. (GREY)
Display the sequence names?
Margin size for the sequence name.
Display the residue number?
Display the date and options used?
Plurality check value (totweight/2) (default is Half the total sequence weighting)
Consensus section
Display the consensus?
Allow collisions in calculating consensus?
Use alternative collisions routine
Print residue scores
Set page to Portrait?
Output section
Output graphic format
Graphic title
Graphic subtitle
X axis title
Y axis title
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.