Search Results for: shortstack

Improving ShortStack performance on highly fragmented genomes

Highly fragmented reference genomes (with thousands or more short contigs or scaffolds) have been a persistent challenge for our small RNA-seq analysis program ShortStack. During a run, ShortStack needs to retrieve genomic sub-sequences for analysis of predicted RNA secondary structure. … Continue reading

ShortStack now on iPlant

A big thanks to Nate Johnson for coordinating the loading of ShortStack 3.3 onto iPlant’s Discovery Environment. There is now a ‘public app’ for ShortStack on the discovery environment. Just search ‘ShortStack’ in the apps. This will allow users to … Continue reading


ShortStack: Alignment, annotation, and quantification of small RNAs 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.  ShortStack discovers … Continue reading

Annotation of miRNAs and phasiRNAs from Norway Spruce

This week I selected a recent article by Xia et al. (2015) titled “Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants” (doi: 10.1093/molbev/msv164, PMID: 26318183) for our journal club … Continue reading

miRNAs in Ectocarpus are a distinct, but share similarities to plants/animals

microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus James E. Tarver, Alexandre Cormier, Natalia Pinzon, Richard S. Taylor, Wilfrid Carre, Martina Strittmatter, Herve Seitz, Susana M. Coelho and … Continue reading

Miscellaneous tools

Below are listed other miscellaneous programs that we’ve released at one time or another. Many of these have all been supplanted with better implementations (either in the latest ShortStack release or the latest CleaveLand4 release)… but in case they are … Continue reading


Major programs Our major and currently actively used programs are hosted at github at . The most important and current ones are ShortStack : Alignment, annotation, and quantification of small RNAs CleaveLand4 : Analysis of degradome data to find sliced miRNA … Continue reading


axtelldata on box cloud storage This folder on Penn State’s cloud storage system has various data sets from older published papers. It also contains testing and tutorial data for ShortStack and CleaveLand4 This server hosts our annotations of small … Continue reading


2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 2020 | back to top MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM … Continue reading

Annotation of Soybean small RNAs reveals non-canonical phased siRNAs

Siwaret Arikit (a,b), Rui Xia (a,b), Atul Kakrana (b), Kun Huang (a,b), Jixian Zhai (a,b), Zhe Yan (c), Oswaldo Valdés-López (d), Silvas Prince (e), Theresa A. Musket (e), Henry T. Nguyen (e), Gary Stacey (c), and Blake C. Meyers (a,b) a … Continue reading