Table 2 List of softwares for plant small RNA research
From: Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs
Software | URL | Description | Reference |
|---|---|---|---|
PlantCARE (a plant cis-acting regulatory element database) | bioinformatics.psb.ugent.be/webtools/plantcare/html/ | Plant gene promoter analysis | (Rombauts et al., 1999) |
PLACE (a database of plant cis-acting regulatory DNA elements) | (Higo et al., 1998) | ||
JASPAR (an open-access database for eukaryotic transcription factor binding profiles) | jaspar.genereg.net | (Mathelier et al., 2016) | |
The MEME suite (containing motif-based sequence analysis tools) | (Bailey et al., 2015) | ||
Bowtie | bowtie-bio.sourceforge.net/index.shtml | An ultrafast, memory-efficient short read aligner | (Langmead et al., 2009) |
Bowtie 2 | bowtie-bio.sourceforge.net/bowtie2/index.shtml | An ultrafast and memory-efficient tool for aligning relatively long sequencing reads to long reference sequences | (Langmead and Salzberg, 2012) |
ShortStack | github.com/MikeAxtell/ShortStack/releases/ | A Perl program for comprehensive annotation and quantification of small RNA genes | (Axtell, 2013) |
NATpipe | Natural antisense transcript prediction | (Yu et al., 2016a) | |
RNAfold webserver | rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi | RNA secondary structure prediction | (Hofacker, 2003) |
RNAshapes | bibiserv.cebitec.uni-bielefeld.de/download/tools/rnashapes.html | (Steffen et al., 2006) | |
miTRATA (microRNA truncation and tailing analysis) | wasabi.ddpsc.org/~apps/ta/index.php | 3′ modification analysis of plant small RNAs | (Patel et al., 2016) |
WebLogo | weblogo.threeplusone.com/ | Search for the conserved sequence motifs | (Crooks et al., 2004) |
psRNATarget (a plant small RNA target analysis server) | plantgrn.noble.org/psRNATarget/ | Target prediction tools for plant small RNAs | (Dai and Zhao, 2011) |
Small RNA Target Prediction | wasabi.ddpsc.org/~apps/tp/ | (Jones-Rhoades and Bartel, 2004) | |
TAPIR (target prediction for plant microRNAs) | bioinformatics.psb.ugent.be/webtools/tapir/ | Not only target prediction, also target mimic prediction for plant microRNAs | (Bonnet et al., 2010) |
comPARE (PARE validated miRNA targets) | Degradome-seq data-based validation for plant microRNA—target pairs | (Kakrana et al., 2014) | |
sPARTA-Web (small RNA-PARE target analyzer) | mpss.danforthcenter.org/tools/mirna_apps/sparta.php | Degradome-seq data-based validation for plant small RNA—target pairs | |
CleaveLand4 | github.com/MikeAxtell/CleaveLand4/releases | A Perl program for degradome-seq data-based validation for plant small RNA—target pairs | (Addo-Quaye et al., 2009) |
agriGO (a GO analysis toolkit for the agricultural community) | bioinfo.cau.edu.cn/agriGO/index.php | Functional analysis of target genes based on Gene Ontology annotations | (Du et al., 2010) |
Cytoscape | www.cytoscape.org | Network data integration, analysis, and visualization | (Shannon et al., 2003) |
Gephi | (Bastian et al., 2009) |