1.Gene Annotation

2. Homolog

3. Jbrowse

4. Tools

5. Download

6. BPG II

1 Gene Annotation

1.1 GeneCard page

BambooBase offers “GeneCard” pages that display comprehensive information about individual genes, along with convenient links to other modules and external databases, all on a single page. The “GeneCard” is organized into two parts. The first part provides essential details about genes, including their unique gene IDs, sequences, structural information, and functional annotations. The second part presents their expression profiles across diverse tissues and developmental stages.

1.2 Search Functions

Users can access the “GeneCard” page by entering a bamboo gene ID in the search box on “Locus Search” page and other annotation search model, such as Go silm search, KEGG search, etc..

1.2.1 Locus search

  1. Select assembly you want to search.
  2. Input gene ID you want to search.
  3. Run the "Locus search" module.

1.2.2 Annotation search

  1. Choose the annotation (GO/KEGG/Pfam/Interpro) search module
  2. Select assembly you want to search.
  3. Input annotation item ID you want to search.
  4. Click the "Search" button.
  5. Choose a interested gene and jump to the GeneCard page.

1.2.1 Experssion search

  1. Select assembly you want to search.
  2. Input genes you want to search.
  3. Select tissues.
  4. Click the "Search" to download gene expression data.

1.2 Transcription Factor

we identified a total of 43,333 genes encoding transcription factors in 68 families.Users can download sequences and view structure of those genes by clicking on the gene family name.

1.3 Repeats Elements

2 Homolog

2.1 Syntelog Groups

  1. Select assembly you want to search.
  2. Input gene ID you want to search.
  3. Run the "Syntelog Group" module.
  4. View syntelogs of target gene in table. The output result includes gene ID, chromosome, start location, end location, and strand.
  5. View and Download phylogenetic tree.

2.1 Ortholog Groups

  1. Select assembly you want to search.
  2. Input gene ID you want to search.
  3. Run the "Ortholog Group" module.
  4. View orthologs of target gene in table. The output result includes gene ID, chromosome, start location, end location, and strand.
  5. View and Download phylogenetic tree.

3 Jbrowse

BambooBase provides gene and TE annotation tracks for all genomes and methylation tracks for D. sinicus, G. angustifolia, P. edulis and Ra. guianensis.The operation guide of Jbrowse 2 can be found here.

4 Tools

4.1 Blast

BambooBase integates SequenceServer to provide an online BLAST service. Users can start from DNA or protein sequences to search in annotated gene databases of 12 bamboo species an Oryza Sativa.

  1. Pasted some nucleotide/protein sequences.
  2. Selected databases and appropriate algorithm for comparing can be auto-detected.
  3. Customize the comparison parameters.
  4. Click.

4.2 Genome Synteny

The "Genome Synteny" module allows users to conveniently select any two bamboo species and visualize their genomic collinear blocks using the dotplotPlugin in Jbrowse 2.

4.3 Micro-Synteny

  1. Select any two bamboo species
  2. Select compared chromsomes
  3. Click.
  4. Select collinear blocks.
  5. View collinear genes.

    6. 4.4 Gene ID Convert

    The “Gene ID Convert tool” enables the linking of gene models across different assemblies of the same species.

    4.5 Enrichment Analysis

    4.6 ORF Finder

    This tool was designed to search open reading frames (ORFs) in the DNA/transcript sequence of interest. The results returned the range of each ORF, along with its protein translation.

    4.7 Primer Design

    Primer designer was designed to help users to build primers that are specific to intended polymerase chain reaction experiments. Primer3 is used to generate the candidate primer pairs for a given template sequence.

    4.8 Co-expression

    The co-expression module provides the results of the co-expression network analysis, derived from 476 transcriptomes utilizing WGCNA. Herein, users can modify the weight threshold parameter, peruse comprehensive tables, and visualize the network.

5 Download

BambooBase is freely available to the public without any registration or login requirements. All the related datasets can be downloaded from the Download module of the database.

6 Bamboo Phylogeny Group II (BPG II)

the BPG II module provides inclusive, integrative and cross-referenced information on the currently accepted 135 genera, with their scientific name, protologue, synonym(s), type species, morphological description, geographic distribution and phylogenetic remarks.