showalign.txt

emboss的linux版本的源代码

                                 showalign 



Function

   Displays a multiple sequence alignment

Description

   showalign displays an aligned set of protein or a nucleic acid
   sequences in a style suitable for publication.

   The output is sent to the screen by default for the user to view, but
   it can write the results to a file.

   The output highlights various differences or similarities between each
   of the sequences and a reference sequence by setting selected types of
   matches to a reference sequence to be '.' characters.

   The reference sequence can be either the calculated consensus sequence
   (the default) or it can be one of the set of aligned sequences,
   specified by either the ordinal number of that sequence in the input
   file, or by its name.

   The output sequences can be displayed in either the input order (the
   default) or they can be sorted in order of their similarity to the
   reference sequence or sorted alphabetically by their names.

   By using the '-show' option, the displayed sequences can either be
   shown as:
     * complete (-show=All),
     * only identical matches between the sequence and the reference
       sequence, all other positions being replaced by '.' characters
       (-show=Identities)
     * non-identical matches, with identical matches being replaced by
       '.' characters, similar matches are shown in lower case
       (-show=Non-identities)
     * similar matches, with non-similar matches being replaced by '.'
       characters, similar matches are shown in lower case
       (-show=Similarities)
     * dissimilar matches, with identical or similar matches being
       replaced by '.' characters (-show=Dissimilarities)

   A small table of the way these alignments are displayed illustrates
   this.
   If we have a reference protein sequence of "III" and a sequence
   aligned to this of "ILW", then we have an identical matching residue,
   then a similar one, then a dissimilar one.
   The different methods of display would give the following:
     _________________________________________________________________

Reference       III

All             ILw
Identical       I..
Non-id          .lW
Similar         Il.
Dissimilar      ..W
     _________________________________________________________________

   Changing the similar matches to lowercase can optionally be disable by
   using the option -nosimilarcase.

   The displayed sequence can be numbered by placing a ruler with ticks
   above the sequence.

   The width of a line can be set. The width of a margin to the left of
   the sequences that shows the sequence names can be set.

   Specified regions of the sequence can be displayed in uppercase to
   highlight them.

   The output can be formatted for HTML.

   If the output is being formatted for HTML, then specified regions of
   the sequence can be displayed in any valid HTML colours.

  The consensus line

   The consensus line can be displayed in a mixture of uppercase and
   lowercase symbols.

   The uppercase consensus symbol is indicates that the consensus is
   strong and lowercase indicates that it is weak.

   The cutoff for setting the case of the consensus is set by the
   qualifier '-setcase'. If the number of residues at that position that
   match the consensus value is greater than this, then the symbol is in
   uppercase, otherwise the symbol is in lowercase. By default, the value
   of setcase is set so that if there are more than 50% of residues
   identical to the consunsus at that position, then the consensus is in
   uppercase.

   To put all of the consensus symbols into uppercase or lowercase, make
   -setcase zero or very large (try 100000 ?).

Usage

   Here is a sample session with showalign


% showalign 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   Display the sequences in order of similarity to the reference sequence


% showalign -order=s 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 3

   Format for HTML and highlight some interesting regions in different
   colours:


% showalign -html -high '4-13 green 43-43 red 51-56 blue' 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 4

   No consensus line at the bottom No ruler line No numbers line Don't
   repeat the reference sequence at the bottom of the sequences Use
   sequence 1 as the reference sequence Display residues from position 10
   to 30 only


% showalign -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 5

   Show non-identities between the sequences


% showalign -show=n 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Example 6

   Show all of the sequences


% showalign -show=a 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 7

   Show identities between the sequences


% showalign -show=i 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 8

   Show similarities between the sequences


% showalign -show=s 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 9

   Show dissimilarities between the sequences


% showalign -show=d 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 10

   Use the first sequence as the reference to compare to:


% showalign -ref=1 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 11

   Show a range of sequences in uppercase, everything else in lowercase


% showalign -nocon -ref=1 -sl -upper 9-15 -nosimilarcase 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 12

   Display the sequences in alphabetic order:


% showalign -order=a 
Displays a multiple sequence alignment
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     The sequence alignment to be displayed.