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Alignment, Similarity, & Database Matching for DNA Motifs

Motif Input

Input Motifs (acceptable formats)
Load motifs from file:

Trim motif edges with information content of less than:

Similarity Matching

Find the best matches to each of your motifs in:
Load user match motifs from file:

Alignment Parameters
Column comparison metric 
Pearson Correleation Coefficient
ALLR
ALLR (Lower Limit)
Sum of Squared Distances
Kullback-Leiber
Description:
Alignment method 
Smith-Waterman
Ungapped Smith-Waterman
Needleman-Wunsch

Gap open and extend:
Overlapping alignments only
Extend the alignment to the edges
Description:
Multiple alignment strategy 
Progressive Profile Alignment
Iterative Refinement
Description:

Tree-building algorithm 
UPGMA
SOTA
Description:

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