RSAT - local-word-analysis

Analysis of oligonucleotide occurrences in a set of DNA sequences.
Program developed by Matthieu Defrance


Sequence       Format Paste your sequence in the box below

Or select a file to upload (.gz compressed files supported)


Mask 
Purge sequences (highly recommended)

Search parameters (motif)
Oligonucleotides of length
Dyads with monad of length and spacing from to

Prevent overlapping matches    Count on     Align

No window (like oligo-analysis or dyad-analysis)
Fixed window of width Group windows
Variable window width (Warning ! this can be time consuming)
Background window width
Background model 
Genome subset  Sequence type     
    Organism  not seeing your favorite organism in the list ? Contact us to have it installed

    Taxon 


Estimate from input sequence
Markov model (higher order dependencies)  order  
Equiprobable residues (usually NOT recommended)

Custom background model

  Create your own background model
Upload your own background file     
    Format 


Thresholds
Fields Lower
Thresholds
Upper
Thresholds
Occurrences
E-value
Significance
Rank
Window rank

Output 
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