Search Databases This page presents a "movie" or "path graph" of alternative Global alignments with near-optimal scores, or with alternate scoring matrices.

Please cite: Michael E. Smoot, Stephanie A. Guerlain, William R. Pearson. 2004. Visualization of near-optimal sequence alignments. Bioinformatics. 20(6),953-958.

Near-optimal Global Alignment

Find Internal Duplications

(A) Sequence type, (B) Sequence 1, (C) Sequence 2, Run an applet example.
(D) Alignment parameters, and (E) Near-optimal neighborhood. Run a Webstart example.

(A) Sequence type: Protein DNA

(B) Enter Sequence 1:    Subset range:
Entrez protein sequence browser

Entrez DNA sequence browser

(C) Enter Sequence 2:  Subset range:

What's the difference?

(D) Alignment Parameters:
Scoring matrix:    open ext

(E) Near-optimal Neighborhood: Upper bound: Lower bound :

Specify a GFF formatted annotation file:

NOTE: Longer sequences and larger the near-optimal neighborhoods take longer to generate the output. Also note that the applet takes a little while to initialize. Please be Patient!

Please report any errors to Be sure to include the alignment parameters used in the report.

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