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Version 1.0
Input sequences
(mandatory)
Genome:
Human
Mouse
Other
Synthetic Genome
Database assembly:
Jan. 2022 (T2T-CHM13 v2.0/hs1)
Dec. 2013 (GRCh38/hg38)
Feb. 2009 (GRCh37/hg19)
Mar. 2006 (NCBI36/hg18)
Upload an ordered list of sequences in BED or FASTA formats:
A list of genomic coordinates in BED format or a list of sequences in FASTA format, ordered by the binding score (descending). The minimal number of input sequences is 5000. In terms of calculation time, we recommend providing the input in BED format.
Clicking on the 'Load sample data' button loads an example of an input list in BED format. The calculation parameters are set to default but can be set differently. By clicking on the 'Submit' button, the job will be submitted and the results will be presented.
Input list loaded:
PUM2_hg19_PARCLIP.bed
Calculation parameters
K
-mer length range:
5-7
Custom range
Min. length:
Max. length:
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.
To select a specific length, select 'Custom range' and insert the same value to both 'Min. length' and 'Max. length' boxes.
Calculate the best motifs based on both sequence and secondary structure (8-letters alphabet)
Calculate the best motifs based on sequence only (4-letters alphabet)
General parameters
Enter a name for the current job (optional):
I would like to get a link to the results by E-mail. E-mail address:
If you use SMARTIV please cite: Polishchuk M, Paz I, Kohen R, Mesika R, Yakhini Z, Mandel-Gutfreund Y. (2017) A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data. Methods. 2017.
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