Software Scripts and console applications miRNATools

miRNA tools

Author: Roman Jaksik

This is a set of Python application used to gather and analyse miRNA sequences. The package includes the following applications:

mimat_ids.py
     Extracts MIMAT ids based on hsa-miR identifiers based on the aliases file from miRBase
miranda_ncl.py
     Extracts miRNA ID, miRNA symbol, transcript ID, and calculates the occurrence of ncl1 vs ncl2 in the seed alignment
mirbase_hairpin.py
     Extracts hairpin structure data from miRBase for each loci ID
mirbase_mature.py
     Extracts mature miRNA sequences from miRBase (latest release) for a specific organism
mirna_seq_targets.py
     Show miRNA targets for a specific sequence combined with their expression levels
mirna_utr_design.py
     Designs an UTR which contains N repeats of the specific miRNA sequence, optionally divided with specific 1-5
     nucleotides in order to reduce the number of other miRNA binding sites.
sequence_similar.py
     Compares all sequences with a multiple sequence alignment using ClustalW2 showing the highest similarity score
     and ID of similar sequence for each sequence on the provided list. Optionally the application can calculate
     expression correlation between pairs of probes. One possible usage of this application is to find similar miRNAs.

The usage description of each application can be viewed by running the application without any parameters.

 

Python scripts: