:: DESCRIPTION
PsRobot is designed to analyze batch of plant small RNA data.
::DEVELOPER
Dr. Xiujie Wang’s “Omics” lab in the Institute for Genetics and Developmental Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W22-8. doi: 10.1093/nar/gks554. Epub 2012 Jun 12.
PsRobot: a web-based plant small RNA meta-analysis toolbox.
Wu HJ, Ma YK, Chen T, Wang M, Wang XJ.
:: DESCRIPTION
Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
H Alexander Ebhardt , Kay C Wiese and Peter J Unrau
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
BMC Bioinformatics 2006, 7:185doi:10.1186/1471-2105-7-185
:: DESCRIPTION
viRome is an R package for the visualization and analysis of viral small RNA sequence datasets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.
Watson M, Schnettler E, Kohl A.
Bioinformatics. 2013 Aug 1;29(15):1902-3. doi: 10.1093/bioinformatics/btt297.
:: DESCRIPTION
ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.
::DEVELOPER
Axtell Lab @ Penn State
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Axtell MJ.
ShortStack: comprehensive annotation and quantification of small RNA genes.
RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112. Epub 2013 Apr 22. PMID: 23610128; PMCID: PMC3683909.
:: DESCRIPTION
srnaloop searchs long DNA/RNA strings for small RNA hairpin loops that may be candidates for small RNA regulatory sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cell. 2003 May;11(5):1253-63.
Computational and experimental identification of C. elegans microRNAs.
Grad Y1, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J.
:: DESCRIPTION
Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oasis: online analysis of small RNA deep sequencing data.
Capece V, Vizcaino JC, Vidal R, Rahman RU, Centeno TP, Shomroni O, Suberviola I, Fischer A, Bonn S.
Bioinformatics. 2015 Feb 19. pii: btv113.
:: DESCRIPTION
segmentSeq is a methods for identifying small RNA loci from high-throughput sequencing data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Feb 15;28(4):457-63. doi: 10.1093/bioinformatics/btr687. Epub 2011 Dec 9.
Identifying small interfering RNA loci from high-throughput sequencing data.
Hardcastle TJ, Kelly KA, Baulcombe DC.
:: DESCRIPTION
sPARTA is a high performance software for the validation of plant miRNA or sRNA targets with PARE (Parallel Analysis of Read Ends) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2014 Oct;42(18):e139. doi: 10.1093/nar/gku693. Epub 2014 Aug 12.
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC
:: DESCRIPTION
CPSS is a web server which provides a comprehensively and systemically integrated pipeline for analyzing small RNA deep sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
CPSS: a computational platform for the analysis of small RNA deep sequencing data.
Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X, Cooke HJ, Xue Y, Shi Q.
Bioinformatics. 2012 Jul 15;28(14):1925-7. doi: 10.1093/bioinformatics/bts282
:: DESCRIPTION
psRNATarget is a plant small RNA target analysis server, which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to “open” secondary structure around miRNA’s target site on mRNA.
::DEVELOPER
The Zhao Bioinformaitcs Lab at the Samuel Roberts Noble Foundation
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W155-9. doi: 10.1093/nar/gkr319. Epub 2011 May 27.
psRNATarget: a plant small RNA target analysis server.
Dai X1, Zhao PX.