Up: Component summary Component

MirMatch

String match for between mature miRNA seeds and target UTR seeds. Mature miRNA seeds are categorized into 8mer, 7mer-A1, 7mer-m8 and 6mer. It does not yet allow G:U wobbles in binding region.

Version 1.0
Bundle sequencing
Categories smallRNA Integration
Authors Ping Chen (Ping.Chen@Helsinki.FI)
Issue tracker View/Report issues
Source files component.xml SeedMatchLib.pm MirMatch.pl
Usage Example with default values

Inputs

Name Type Mandatory Description
utrSeeds CSV Mandatory A CSV file contains UTR seed sequences. The sequences have orientation of 5'-3'. The first column is identifier and the second column is the sequence.
matureSeq CSV Mandatory A CSV file contains all mature miRNA sequences with orientation of 5'-3'. The first column should be identifier and the second column should be sequences.
pairs CSV Mandatory A CSV file contains the candidate interaction between mature miRNA and its targets. Transcripts of the input 'utrSeeds' must exist in this file.

Outputs

Name Type Description
matched CSV A CSV file for matched seeds. It has columns 'SeedID', 'TranscriptID' and 'miRNA'.
Generated 2019-02-08 07:42:12 by Anduril 2.0.0