PPR: annotate simultaneously
all protein motifs known to appear in the PentatricoPeptide Repeat
protein family. Produce a single alignment with all motifs
deltimited in it. Access on-line.
STAR: Search for Approximate Tandem
Repeats in a DNA sequence. Access on-line or download the executables.
MS_Align:
Pairwise alignment of minisatellite maps.
2ZIP: prediction of Leucine
Zipper domain from the protein sequence. Access on-line or download the package.
GeneNest:
gene indices for human, mouse, zebrafish and Arabidopsis thaliana.
Browse them with a nice interface.
Transformation Distance:
pairwise compare sequences and reveal segment inversions,
duplications.
SearchRepeats: detection of
exact repeats by a compression algorithm.
QUASAR:
a fast sequence similarity search algorithm for multiple queries.
If you find these softwares useful, please cite the
corresponding articles. The complete references are in my
Publication List