microRNA target prediction

microRNA target prediction
from RNA duplexes

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Running MicroTar

Mandatory Command Line Flags

Use the following syntax to run MicroTar:

microtar -t mRNA.fa -q miRNA.fa

where mRNA.fa is a Fasta-formatted file of mRNA (target) sequences, and miRNA.fa is a Fasta-formatted file of microRNA (query) sequences. All mRNA sequences will be scanned against all microRNA sequences.

If you wish to restrict microRNA binding to mRNA 3'-UTRs (recommended), ensure that the Fasta-formatted mRNA sequence has its coding region in uppercase and UTR in lowercase. A perl script is available to convert GenBank files into appropriately formatted Fasta files. This scipt uses the Bio::Seq and Bio::SeqIO modules from the BioPerl project.

Optional Command Line Flags

These may be used individually or in combination.

  • To produce a tab-separated output file of seed matches and energies, supply a file name with the '-f' flag:
    microtar -t mRNA.fa -q miRNA.fa -f results.tsv
  • To produce scalable vector graphic images of mRNA secondary structures before and after miRNA binding, use a '-i' flag (serial version only):
    microtar -t mRNA.fa -q miRNA.fa -i