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microRNA-targets

This Python script is used to find potential animal miRNA seed binding sites. Basically, this script is used to find a small RNA sequence pattern (6-8 characters long) in a database of longer RNA seqences. For fast searching, longer RNA sequences are stored in a hash table.

input arguments:

It takes 3 parameter: target sequences (Fasta file), miRNA sequences (Fasta file) and seed length(6,7 and 8).

target sequences/miRNA files should be in FASTA format as follows

>sequence_id 
ATCTGTTTGTCAA

"id" will be used in the output files.

seed length

6 => sequence starting at position 2 (from 5' side of miRNA seq.) to position 7

7 => sequence starting at position 2 (from 5' side of miRNA seq.) to position 8 *** Recommended***

8 => sequence starting at position 1 (from 5' side of miRNA seq.) to position 8

Output files

  1. 7mers.txt (If you choose seed length = 7, each row represents a miRNA-3'UTR pair. It gives info. about how many sites are in the target sequence and p-Value indicating how likely to see this number of hits in this region.

  2. 7mers_hits.txt: gives info. about individual hit (start position of the hit in the target region).

Example run on Linux command line:

python3 miRNA_targets_v0.3.py   3utr.fasta miRNA_sequences.fasta      7