A comprehensive and integrated database could provide coherent information to users and advance either scientific or practical progresses. ANA-grade plant Genome & Taxonomy Database (ANAGDB), which integrates the ANA-grade plant data from public databases with the data produced by our group. The ANAGDB combines a variety of multi-omics data (genome, miRNA, and transcriptome) and taxonomic resources with a wealth of phenotypic images. In addition, ANAGDB offers a couple of easy-to-use access functions/interfaces and eight built-in tools for data analysis, for instance, Blast, JBrowse, Search Gene, Tissue Expression, Gene Annotation, Primer Design and Literature. Therefore, we believe that ANAGDB, a comprehensive database with useful data on genome, genotype, and taxonomy, may represent a valuable resource for the entire ANA-grade research community.
1. Click on “FTP Download” to obtain assembly and annotation files. 2. Click on “Blast” then jump to Blast interface.
Taxonomy Search Box 1. Search box: three arguments for searching taxonomy by Scientific name, Authority or REF. 2. Result box: showcase for filtered taxonomy. 3. Download file including all taxonomy information.
The transcriptome page shows the expression levels of certain genes (queried genes) under different tissue and treatment conditions.
1. Select the species you want to view in the Genome column;
2. Select the tissue or treatment method of the species in the Tissue & treatment column;
3. Enter the Gene ID you want to query here;
4. The results show a heatmap of expression levels for the query gene cluster. The shade of color usually represents the level of expression, with blue representing low expression and red representing high expression;
5. Gene line chart: A line chart shows the trend of the expression levels of selected genes changing with time or conditions under different tissue conditions;
6. Expression values of genes: Lists specific gene IDs and their expression values under various tissue conditions;
7. Raw data: Provides detailed information on the samples used for RNA-Seq, including tissue or processing conditions, related biological projects (Bioproject), sequencing libraries used (Library), and RPKM values of sequencing reads.
1. Species drop-down menu: Select the species you want to query through this column;
2. Data type: "MIR family", "MIR loci", "clusters", and "sRNA-Seq data", etc;
3. Download: These buttons allow users to download selected data. After selecting a target sequence, "Download Selected" will download only the checked entries, while "Download All" will download the entire dataset shown.
1. Enter DNA sequences or upload sequence fasta file for blastn, tblastn and tblastx; AA sequences for blastp and blastx.
2. Select the blast program to run.
3. Select the species sequence to run blast on.
1. Searching gene by inputting a gene id. e.g. Amtri01G0001900.
2. Obtaining the sequences of queried gene, including CDS and protein.
3. An interactive mode of gene structure. Blue boxes represent exons. Black lines represent introns. An arrow indicates transcription direction. Double-stranded DNA sequences corresponding to horizontal scroll bar exhibit in the black box.
1. Search box: inputting a gene name, e.g. Amtri01G0001900.
2. Bar chart showing the average expression level of queried gene in green fruit, red fruit and leaves of different developmental stages.
3. Heat map showing the expression level of queried gene in certain RNA-seq libraries.
InterproScan was implemented to annotate gene from 5 ANA-grade plants genomes. Users just need to input a gene id, then click on button "Search".
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.
ANAGDB integrates a modified version of primer3, by which users only need to input a gene id before selecting mRNA in the pull-down menu (see red box). Then, clicking on the button “Get sequence”, the sequences will be filled in automatically.
1. Searching box for literature regarding to ANA-grade: User could search studies related to ANA-grade from over 800 publications by four options, including year, author, title, and journal.
2. Result table: Clicking on a title, then jumping to the full text of this paper.
Tools