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
Posted in ShortStack
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
Posted in ShortStack
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
Posted in Uncategorized
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
Posted in Journal Article
Software
Major programs Our major and currently actively used programs are hosted at github at https://github.com/MikeAxtell . 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
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Publications
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 2024 | back to top Trans-species mobility of RNA interference between … Continue reading
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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
Posted in Journal Article
plantDARIO – a web-based tool for small RNA-seq analysis in select plant genomes
Patra et al. (2014). plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. Frontiers in Plant science. doi: 10.3389/fpls.2014.00708 PMID: 25566282 This manuscript describes a web-based service for the annotation of small RNA-producing genes in Arabidopsis … Continue reading