(DEBUG version)
Version 2.0
Input sequences
Species:            Genome assembly:
Upload sequences as A list of sequences in .BED format or .FASTA format (must contain at least 2000 sequences of more than 20 nucleotides). Input sequences should be one of:
  • ordered by sequence binding score in descending order (i.e. higher binding signal/noise ratio sequences at the top)
  • be in a format that contains sequence binding score (ENCODE narrowPeak, BED 6-column format, or FASTA with headers that have coordinate, strand, and score)
Loads list of sequences in BED format for PUM2 dataset obtained from PAR-CLIP experiment. Parameters are set to default but can be edited. By clicking on the 'Submit' button, the job will be submitted and results presented.
Calculation parameters
Extract combined sequence & structure motifs (in 8-letter alphabet)   
        Folding method:
Extract sequence motifs (in 4-letter alphabet)
K-mer length range: SMARTIV can search motifs in a specific length or in a range. The length refers to the enriched k-mers composing the PWM. The maximal length range allowed is 4-10 characters.    
Optional parameters
Job name:
Get results by E-mail address:
If you use SMARTIV please cite both:
  1. Polishchuk M, Paz I, Yakhini Z, Mandel-Gutfreund Y. SMARTIV: Combined sequence and structure de novo motif discovery for in vivo RNA binding data. Nucleic Acids Research. 2018. [PMID: 29800452] [pdf]
  2. Polishchuk M, Paz I, Kohen R, Mesika R, Yakhini Z, Mandel-Gutfreund Y. A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data. Methods. 2017. [PMID: 28274760] [pdf]