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miRiam is a fast and reliable tool for screening miRNA databases in order to identify potential interactions with a given mRNA. It is based both on thermodynamics features and empirical rules coming from known interactions.
miRiam accept a mRNA sequence as input and returns the list of possible interactions between the sequence and miRNAs from a selected database. By default, miRBase is used, but users can also choose to provide their own list of miRNAs.
Although the default settings are optimized for standard usage, miRiam allows users to specify several parameters, concerning target accessibility evaluation and empirical rules application.
The miRiam package contains:
All these components are necessary. You will also need Python interpreter. It usually comes with every Linux distribution. You can get the latest version at www.python.org.
For a correct installation, please follow these steps:
A) Install the Vienna RNA Package.
C) Install miRiam:
The easiest way to use miRiam is by the following command line:
where source is a short code that indicates the organism-specific subset of miRBase to be screened (Ex. Homo sapiens=hsa, Mus musculus=mmu, …), and target is the name of a file which contains the target mRNA sequence in Fasta format.
This will perform a complete search for potentially accessible binding sites on bcl2 3' UTR for all the Homo sapiens miRNAs in miRBase, returning the corresponding miRNA/mRNA duplexes.
3'UTR start position will be obtained by computing the longest ORF. The output file will be bcl2_miriam.txt.
(The bcl2.fasta example file is located in the examples directory)
* If the command does not work, try:
A number of useful options are listed below:
This will perform a complete search for most potentially accessible binding sites on hoxb8 3' UTR for all the Homo sapiens miRNAs in miRBase, returning the corresponding miRNA/mRNA duplexes. The 3'UTR start position is given in input. A free filter scheme is used, allowing only 1 G:U wobble and no mismatches in the seed region of 9 nucleotides.
This will search for potentially accessible binding sites on the whole bcl2 sequence for the Homo sapiens miRNA miR-15a, returning the corresponding miRNA/mRNA duplexes. A relaxed filter is used, allowing up to 3 mismatches and 2 G:U wobbles in the seed region of 7 nucleotides. The output file will be bcl2_miriam.txt.
This will perform a complete search for potentially accessible binding sites on lin28 3' UTR for all the miRNAs in the provided list (my_mirnas.txt – See Appendix A for the right format) returning the corresponding miRNA/mRNA duplexes. 3'UTR start position will be obtained by computing the longest ORF. The output file will be lin28_miriam.txt.
(The hoxb8.fasta, lin28.fasta and my_mirnas.txt example files are located in the examples directory)
The miRBase files can be easily updated. To do so, download the latest version from http://microrna.sanger.ac.uk/sequences/ftp.shtml, put the mature.fa file in the miRiam directory (by default miriam), and run the DBinit routine:
This will cause the update of miRBase files in the mirdb directory. All previous files will be overwritten by the new ones.
A custom miRNA database can be provided via the mirdb option.
The file must be in the following format:
Here is an example: