Degradome sequencing data analysis bioinformatics software tools
Parallel analysis of RNA ends (PARE) is a high-throughput sequencing technique which profiles uncapped mRNAs, products of cleavage or decay, facilitating studies of miRNA targets (German et al., 2009). Nearly identical techniques have been termed ‘degradome analysis’…
G T A T C G C T A
sPARTA package
Desktop

sPARTA package

A powerful tool for plant miRNA target prediction and PARE validation. It can…

A powerful tool for plant miRNA target prediction and PARE validation. It can search for targets in unannotated genomic regions, which is useful to discover novel regulatory modules, independent of…

G T A T C G C T A
miRNA Digger
Desktop

miRNA Digger

A pipeline for large-scale identification of miRNA candidates through…

A pipeline for large-scale identification of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA…

G T A T C G C T A
StarScan
Web

StarScan sRNA target Scan

An integrated web-based tool for scanning sRNA targets using degradome…

An integrated web-based tool for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, StarScan performs an ultrafast and exhaustive…

G T A T C G C T A
piPipes
Desktop

piPipes

A coordinated set of pipelines, 'piPipes', to analyze piRNA and…

A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or…

G T A T C G C T A
PAREsnip
Desktop

PAREsnip

A fast user-friendly multi-platform bioinformatics tool to find targets of…

A fast user-friendly multi-platform bioinformatics tool to find targets of small RNAs using the degradome.

G T A T C G C T A
CleaveLand
Desktop

CleaveLand

A generalizable computational pipeline for the detection of cleaved miRNA…

A generalizable computational pipeline for the detection of cleaved miRNA targets from degradome data.

G T A T C G C T A
MTide
Desktop

MTide

By searching for targets of a complete miRNAs, it can facilitate large-scale…

By searching for targets of a complete miRNAs, it can facilitate large-scale identification of miRNA targets, allowing us to discover regulatory interaction networks.

G T A T C G C T A
SeqTar
Desktop

SeqTar SEQuencing-based sRNA TARget prediction

A computational method that allows more mismatches and critically mismatch or…

A computational method that allows more mismatches and critically mismatch or G:U pair at the position 10 or 11. Precisely, two statistics were introduced in the program, one to measure the alignment…

Related Websites
Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.