Belvu Homepage

What is Belvu?

Belvu is an X-windows viewer for multiple sequence alignments. One of the main advantages of Belvu is that it has an extensive set of modes to color the residues. There are several ways to color them by conservation and by residue type (user-configurable). Other useful features are fetching of the Swissprot (or PIR) entries by double clicking and easy tracking of the position in the alignment.
Belvu further supports some simple editing commands for rows and columns, but is not intended as a full editor. For actually editing the alignment, use your favorite alignment editor or Emacs.

How to run Belvu

Type 'belvu' to get brief help:

Belvu - View multiple alignments in pretty colours.

 Usage: belvu [options]  < multiple_alignment > | -  [X options]

 < multiple_alignment > | - = file or pipe in Pfam/selex/MSF format (see below).


 Options:

 -r           Alignment is in 'raw' format.

              Example of raw alignment file: 

                  seq1_name MFILKTP
                  seq1_name MYI.RTP

 -l < file >  Load color code file.

              Format: < symbol > < color >
              (Lines starting with # are ignored (comment lines))

              Example of color code file:

                  # Aroma
                  F YELLOW
                  Y YELLOW
                  W YELLOW

		  # Yuck
                  D RED 
                  N GREEN  
                  X BLUE

              Available colors:

                    WHITE 
                    BLACK 
                    LIGHTGRAY 
                    DARKGRAY
                    RED 
                    GREEN 
                    BLUE
                    YELLOW 
                    CYAN 
                    MAGENTA
                    LIGHTRED 
                    LIGHTGREEN 
                    LIGHTBLUE
                    DARKRED 
                    DARKGREEN 
                    DARKBLUE
                    PALERED 
                    PALEGREEN 
                    PALEBLUE
                    PALEYELLOW 
                    PALECYAN 
                    PALEMAGENTA
                    BROWN 
                    ORANGE 
                    PALEORANGE
                    PURPLE 
                    VIOLET 
                    PALEVIOLET
                    GRAY 
                    PALEGRAY
                    CERISE 
                    MIDBLUE


 -c           Print Conservation table.

 -a           Sort sequences alphabetically.

 -s < file >  Read in file of scores.  A column with scores will
              automatically appear after the coordinates.

              Format: < score > < sequence_id >

              Example of score file:

                  2.78 seq_1/180-206
                  2.78 seq_2/180-206
                  3.79 seq_3/42-94
              
 -o           Output alignment in Pfam format.

 -t < title > Set window title.

 -g           Draw grid line (for debugging).

 -m < file >  Read file with matching sequences segments. This is used to
              display a match of  a query sequence to a family.  The format
              of the match is :

              Line 1: Name/start-end score
              Line 2: Query sequence in matching segment, no pads!
              Line 3: Sequence of matching segments (qstart1 qend1 fstart1
              fend2 qstart2 qend2 fstart2 fend2  etc...).

              Example:

              ZK673.9/238-385 21.58
              CPENWVQFTGNGTQYGVCLRGFTATGGSYGYQHAIDYCASEVKNAHLANEFSQAKHDFMQILMAISFPKYKPLEYYIGLRNLGNQWLWEQPQGQDMIPLNPLIYSKWAPGFPQANSTNQVISTQPLQEGSTDFFWAPPQTNDWLFICQ
              1 2 1 2  4 7 8 11  8 15 14 21  16 17 23 24  27 43 28 44  44 57 46 59  58 67 61 70  74 83 80 89  84 94 95 105  100 108 109 117  109 112 121 124  113 125 133 145  128 134 149 155  138 143 158 163  144 148 165 169  

              NOTE: A sometimes easier way of doing this is to concatenate
              the match to the end of the alignment, after a line with
              exactly this string within the quotes: "# matchFooter"


 Some X options:

 -acefont < font >   Main font.
 -font    < font >   Menu font.

In other words, to get going, just type 'belvu my_alignment' and it should work. It detects if it is in MSF, selex or Pfam format (see below), but you have to tell it if it is in 'raw' format (Name sequence).
The file of scores should be in the format "score name" with one score per sequence name in the alignment on a separate line.

NOTE: Make sure that all sequence names are unique - very funny thing happen if they are not.

Multiple alignment file formats supported by Belvu

Belvu currenty supports MSF, selex and Pfam formats. Selex is the native format used by Sean Eddy's HMM package HMMER. The Pfam format is Pfam's native format, and has one domain per line like this: "Seqname/start-end SEQ.UENCE". The residues must be aligned and gaps should be represented by dots.

Note on the MSF format: The "..... Check: .." line has to come before the first line that does not start with a space. The only legal exception is the line "PileUp of:" from GCG programs.

Last edited: Feb 7 1996 (esr@sanger.ac.uk)