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