Zhang T, Zhai J, Zhang X, Ling L, Li M, Xie S, Song M, Ma C. Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA.
Genomics Proteomics Bioinformatics. 2021 Jul 28:S1672-0229(21)00161-3. doi: 10.1016/j.gpb.2021.02.010. Epub ahead of print. PMID: 34332120.
Guo Z, Kuang Z, Wang Y, Zhao Y, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T, Cao X, Wei J, Li L, Yang X. PmiREN: a comprehensive encyclopedia of plant miRNAs.
Nucleic Acids Res. 2020 Jan 8;48(D1):D1114-D1121. doi: 10.1093/nar/gkz894. PMID: 31602478; PMCID: PMC6943064.
miRPlant extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants.
TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information.
rTASSEL construct an R-based front-end to connect to a variety of highly used TASSEL methods and analytical tools.
iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. Identification and classification of TFs and TRs are based on the rules (required and forbidden protein domains of each gene family) described in Perez-Rodriguez et al (2010).