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’…
Desktop app
G T A T C G C T A sPARTA package sPARTA package

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…

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

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…

Web app
G T A T C G C T A sRNA target Scan sRNA target Scan

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…

Desktop app
G T A T C G C T A piPipes piPipes

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…

Desktop app
G T A T C G C T A PAREsnip PAREsnip

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.

Desktop app
G T A T C G C T A CleaveLand CleaveLand

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.

Desktop app
G T A T C G C T A MTide MTide

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.

Desktop app
G T A T C G C T A SEQuencing-based sRNA… Deprecated SEQuencing-based sRNA TARget prediction

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…

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