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Formatting Multiple Alignments

The final product of a PILEUP or CLUSTAL run is a set of aligned sequences, which are stored in a Multiple Sequence File (called .msf by GCG).

This msf file is a text file that can be formatted with a text editor, but GCG has some dedicated tools for improving the looks of msf files for easier interpretation and for publication.

Consensus sequences can be calculated and the relationship of each character of each sequence to the consensus can be highlighted using the program PRETTY .

PRETTY takes the output of PILEUP as input but - and here is another silly GCG weirdness - you must follow the file name with an asterisk in curly brackets {*} like this:

$ PRETTY  myseqs.msf{*}

You will probably want to add some modifiers to the command line.

• add /CON to create a consensus sequence
  
  
• use /CASE to type characters that match the consensus in uppercase and others in lowercase
  
  
• use /DIFF to type only those characters that do not match the consensus

So a typical command line for PRETTY would look like this:

$ PRETTY/CON/DIFF  myseqs.msf{*} 

Shading of regions of high homology can be created using the program BOXSHADE, but this is not actually part to the GCG package and it is a bit complex to use.

GCG has combined most of the functions of PRETTY and BOXSHADE into a new program called PRETTYBOX in GCG v.10. Just use the command PRETTYBOX instead of PRETTY to format a mutliple alignment file and you will get a fairly nice shaded alignment.

$ PRETTYBOX  myseqs.msf{*}

In addition to these programs that run on the Alpha, the output of PILEUP (or CLUSTAL) can be moved by FTP from your RCR account to a local Mac or PC.

Since this output is a plain text file, it can be edited with any word processing program, or imported into any drawing program to add boldface text, underlining, shading, boxes, arrows, etc.

There is also a Macintosh version of the BoxShade program called MacBox.

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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center

Comments to: browns02@mcrcr.med.nyu.edu