mirnamotif

miRNAmotif is an application that enables the user to

• search for specific motifs in the terminal loop, linking sequence (sequence between mature miRNAs from two arms), mature miRNA or in whole pre-miRNA among sequences in a widely used miRNA database (miRBase) and
• predict enriched motifs within sequences provided by the user.

miRNAmotif is a simple and user-friendly application that gives researchers the opportunity to analyze known pre-miRNAs sequences for the presence of specific motifs that can be recognized by protein regulators of miRNA biogenesis.

Licence

This application is open-source under MIT License (see LICENSE file)

Availability

Webserver

Webserved is freely available at http://mirnamotif.ibch.poznan.pl/

CLI

Database preparation

Files with miRNAs, linking sequence, loops and pre-miRNAs are already build from hairpin.fa, hsa.gff3, mmu.gff3, ath.gff3 and mature.fa but when needed they can be rebuild with new hairpin.fa, hsa.gff3, mmu.gff3, ath.gff3 and mature.fa files (files need to be in mirnamotif folder) running python ./mirnamotif/parser.py

Running mirnamotif - search for known motif

To find premirnas with single motif using mirnamotif run python ./mirnamotif/mirnamotif.py GGAG and python ./mirnamotif/mirnamotif.py GGAG -s AGG for two motifs search.

To see options for this function please see python mirnamotif/mirnamotif.py --help

Options are: python ./mirnamotif/mirnamotif.py GGAG [-s AGG] [-t loops|sh|linking|mature] [-d f|fr] [-o True|False] [-db hsa|mmu|ath] [-fp file_prefix]

e.g. python ./mirnamotif/mirnamotif.py GGAG -s AGG -t linking -d fr -o False -db mmu -fp mmu_linking

Results will be saved in ./mirnamotif/results/ localization with day and hour within filename.

Running mirnamotif - search for new motif

To be able to search for new motifs, meme suite is needed. Please download 4.11.4 version of meme http://web.mit.edu/meme_v4.11.4/share/doc/download.html into the same folder as repository, unpack the archive file and follow the instructions from INSTALL file.

After meme installation you can look for new motifs using command python ./mirnamotif/mirnamotif_find.py ./static/example_motif.txt -f ./results/new_meme_results -db sh

First argument is a file directory with names of precursors (e.g. mmu-let-7k) or sequences. Optional arguments include folder to save results, orientation and whether sequences searched should be loops or whole pre-miRNAs.

To see options please see python ./mirnamotif/mirnamotif_find.py --help.

Options are: python ./mirnamotif/mirnamotif_find.py ./static/example_motif.txt [-d f|fr] [-db sh|sh_ath|sh_mmu|sh_hsa|loops|loops_ath|loops_hsa|loops_mmu|mature|mature_ath|mature_hsa|mature_mmu|linking|linking_ath|linking_mmu|linking_hsa] [-f ./results/new_meme_results] [-n directory_to_negative_sequences]

Please remember that -n overwrites -db option.

e.g. python ./mirnamotif/mirnamotif_find.py ./static/example_motif.txt -d fr -db linking_hsa -f ./results/new_meme_results

Authors

Martyna O. Urbanek-Trzeciak

Edyta Jaworska

Wlodzimierz J. Krzyzosiak

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland

Citation

Urbanek-Trzeciak, M.O.; Jaworska, E.; Krzyzosiak, W.J.

miRNAmotif—A Tool for the Prediction of Pre-miRNA–Protein Interactions.

Int. J. Mol. Sci. 2018, 19, 4075.

https://doi.org/10.3390/ijms19124075

Contact

For any issues, please create GitHub Issue or contact us under mirnamotif at gmail.com

Funding

This research was funded by the Polish National Science Centre (2015/17/N/NZ3/03629)