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Editing Multiple Alignments

Multiple sequence alignment is a mathematically complex process. For a given group of sequences there is no single "correct" alignment, only an alignment that is "optimal" according to some set of measurements.

The multiple alignment programs such as PILEUP and CLUSTAL rely on approximations, so it is not even possible to be sure that the alignments they produce are truly optimal.

Determining what alinment is best for a given set of sequences is really up to the judgement of the investigator.

You should feel free to tweak the parameters used by the alignment programs (gap penalties, protein scoring matricies, etc), but also to adjust the alignment itself to conform to your ideas about the relationships among the sequences.

There are a variety of multiple sequence editors that can be used to modify a multiple alignment.

These programs can be very useful in formatting and annotating an alignment for publication.

An editor can also be very useful to make some modifications by hand to improve biologically significant regions in a multiple alignment created by one of the automated alignment programs.

Multiple alignments created with PILEUP or CLUSTAL (MSF format) can be edited with LINEUP and consensus sequences can be created with PRETTY.

GCG's SeqLab X-Windows interface has a superb multiple sequence editor - the best of any kind.

The MACAW and SeqVu program for Macintosh and >GeneDoc and DCSE for PCs are free and provide excellent editor functionality.

There is also a program offered on the Web for editing multiple alignments called CINEMA (Colour INteractive Editor for Multiple Alignments) which has been created completely in the JAVA computer language.

From the CINEMA homepage, , the CINEMA program can be launched as a self-contained "applet" which runs as a program on your desktop computer (not on the web server).

DNA and protein alignments are edited by clicking on the sequences and dragging them to create gaps; whole sequences may be shifted to the left or right by clicking on the right mouse button and dragging.

Amino acid sequences are colored according to residue type (acidic, basic, aromatic, etc.).

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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