Software Developer: Chengjie Chen
TBtools is a stand-alone software with a user-friendly interface which is a Toolkit for Biologists integrating various biological data-handling tools. The toolkit incorporates over 130 functions, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine (‘‘JIGplot’’) developed to maximize their interactive ability. Meanwhile, TBtools is an integrative and interactive toolkit with cross-platform compatibility, which is compatible with the three major operating systems (Windows, MacOS, Linux).
TBtools is developed for wet-lab biologists. It contains an extensive collection of functions, which are integrated into a user-friendly graphic user interface (GUI) that can be easily navigated using point-and-click icons. For each function in TBtools, we designed a GUI panel according to the most straightforward IOS logic, i.e., Set Input Data, Set Output Path if Required, and Click Start Button.
Since the exploitation of TBtools,the tool has attracted over 20,000 stable users.
Software Developer: Guanliang Li & Chengjie Chen
sRNAminer is a cross-platform software with a Graphical User Interface (GUI) which can be run under Linux, MacOS, and Windows. Moreover, we also provide a command-line version for users to analyze large data on servers.
Notably, sRNAminer covers different types of sRNA analysis with data browsing function. The functions of sRNAminer are divided into three main parts: (1) Data pre-processing. This part includes four steps, from Adapter Trimming and Sequence Collapsing to Data Cleaning and Genomic Mapping. (2) sRNA identification and expression calculation, which can be performed for three main types of sRNAs,including miRNA, phasiRNA and hc-siRNA.(3) Other common functions, including sRNA target prediction, PHAS trigger identification, degradome analysis, and etc.
IGV-sRNA is a powerful sRNA data visualization tool that we developed. As compared to the original IGV software, it provides numerous additional functions specialized for plant sRNA profiling, including secondary structure visualization, calculation of the phasing score on-the-fly, and read length visualization in a color-coded dot plot. The same color scheme for sRNA length can also be applied to the visualization of sRNA genomic alignment, allowing users to easily detect the distribution pattern of sRNAs with different lengths. To ensure a more flexible and convenient browsing of sRNA data, the "sRNA viewer" function in sRNAminer is designed to interact with IGV-sRNA.
Database developer: Jiawei Li & Chengjie Chen
SapBase (www.sapindaceae.com) provides genomic resources and an online powerful analytic platform for scientific research on Sapinaceae species and comparative studies of plants. SapBase integrated NGS data with all publicly available data for seven Sapindaceae plants and constructed the Sapinaceae Genomic DataBase, including full genome sequences, resequencing genomic data, RNAseq data and sRNA loci from the sRNAanno database.
All data are accessible at SapBase via the four major function categories: BROWSE for data and result browsing; SEARCH for comprehensive and efficient information retrieval; ANALYSES providing various data processing, analysis and visualization functions, and DOWNLOAD for data deposit and download.
Database developer: Jiawei Li & Chengjie Chen
Small RNAs (sRNAs) are essential regulatory molecules in plants. The sRNAanno database hosts a large collection of miRNA, phasiRNA- and hc-siRNA-generating loci annotated from ~140 plants using consistent and high-confident criteria. All the annotations are made freely available to the scientific community via various services and tools.
Comparing to other public plant sRNA databases, sRNAanno provides much more miRNA annotations, which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations.sRNAanno also provides free access to genomic information for >22,721 PHAS loci and >22 million hc-siRNA loci annotated from these 143 plant species. Both miRNA and PHAS loci can be easily browsed to view their main features, and a collection of archetypal trans-acting siRNA 3 (TAS3) genes were annotated separately for quick access. To facilitate the ease of sRNA annotation,sRNAanno provides free service for sRNA annotations to the community.
In summary, the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs.
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