Display of Near Optimal Sequence Alignments
M. Smoot1, W. Pearson2 and S. Guerlain1
University of Virginia
Department of Systems and Information Engineering, School of Engineering and Applied Science (1)
Department of Biochemistry and Molecular Genetics, School of Medicince (2)
Charlottesville, VA 22904-4747
Contact: {mes5k,wrp,guerlain}@virginia.edu
www.sys.virginia.edu/hci
1. Introduction
2. Current Display
The biological meaningfulness of alignments generated by optimal
sequence alignment algorithms (e.g. Smith-Waterman) has been
questioned for years. It has been speculated that the biologically
optimal alignment of two sequences lies somewhere near the
algorithmically optimal solution. While various algorithms have been
proposed for generating near optimal solutions, none of these
methods provide a mechanism for effectively finding the most
meaningful alignment. The primary problem is that there is often a
large number of similar solutions generated.
• Hard to compare
sequences at the
base/aa level.
• Hard to know
which alignments
are most
important.
• Hard to know how
many alignments
exists
We have developed a web based software system for the creation
and display of near optimal or alternative alignments of two protein
or DNA sequences. The tool is designed to help investigators identify
the most biologically meaningful alignment of two sequences.
3. System Prototype
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Web Based Interface.
Alignments displayed sequentially, like a movie.
Mulitple optimal and near optimal alignments generated.
Multiple combinations of scoring matrices, gap parameters and neighborhood
thresholds allow users to generate comprehensive sets of alignments.
User specifiable and controllable highlighting.
Steady display keeps aligned regions in the same screen location so that the
parts of the alignments that are relatively invariant appear that way.
Works with DNA and Protein.
Allows investigators to use expertise instead of relying on algorithms.
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Followed a user-centered design process in developing an interface.
System prototype developed using C++, Java and Perl.
Can fetch sequences from NCBI, upload sequences or allow pasted sequences.
Will integrate annotation information from external databases (NCBI, SwissProt,
etc.)
• Evaluation in progress.
Movie controls
Shades of orange indicate variation of
different regions of alignment.
Display option selection
Different Highlights, including user configurable highlights.
Sequence and alignment information
Alignment generation information
Prototype available at:
www.sys.virginia.edu/hci/research.html
5. Acknowledgements
This work was supported by the University of Virginia Biotechnology Training Program (sponsored by NIH)