Documents

Manual

1 Search

1.1 Simple search

1.2 Advanced search

2 Browse

2.1 Functional annotation

2.2 MicroRNA data and RNA-seq data

3 Tools

3.1 Pathway

3.2 PPI

3.3 GBrowse

3.4 BLAST

3.5 BLAST2seq

3.6 Retrieve Sequences

3.7 Comparative Genome Search

4 Documents

5 Download

1 Search


1.1 Simple search

BambooGDB provide simple search in Home page or search page.

First,take “PH01000087G0720” as an example.

In Home page:

In Search page:

Then, both results above will link to identical Result page as the following.

Finally, click “PH01000087G0720” will enter “gene card”,which include a graphical view of the local genomic environments and three tabs. In the first tab, fundamental annotation information were contained such as gene/protein name, length and location, expression profiles, heterozygous SNPs, ortholog group and best arabidopsis/rice hit by best match of arabidopsis/rice protein sequence BLASTP against protein of moso bamboo. In the second tab, comprehensive functional and structural feature of moso bamboo were highlighted. In the three tab, the relative sequences information of individual gene were presented and conveniently downloaded by developed clipboard function. Additionally, many internal crosslinks were provided to efficiently access related tools in each tab.

Tab 1

Tab 2

Tab 3

1.2 Advanced search

BambooGDB have provided advanced search with a Boolean search to allow users to specify and combine query options by functional characterizations, such as COG, InterPro, Gene Ontology, EC number and Pathway information.

First, take “COG1287” and “GO:0004576” as an example.

Then, the result will link to identical Result page as the following.

2 Browse


2.1 Functional annotation

BambooGDB also provides efficient presenting information with identical functional classification such as pathway, enzyme, COG and top hit.

Firstly, take “pathway” as an example.

Then, the result will link to Result page as the following.

2.2 MicroRNA data (putative) and RNA-seq data

In BambooGDB, the previously and valuable results for genomic analysis were displayed such as RNA-Seq and predicted miRNA data.

Take “RNA-seq” part as an example.

3 Tools


3.1 Pathway

Based on the KEGG database, genes of moso bamboo were annotated with the KEGG orthology (KO) by using the best hit information. In addition, the graphical display employed KEGG Automatic Annotation Server (KASS) can visually help user to efficiently understand the characteristics of metabolic pathways.

Firstly,take “[PATH:ko00010] Glycolysis / Gluconeogenesis” as an example.

Then, the result page see the following.

3.2 PPI

As an important aspect of current proteomics research, protein-protein interactions (PPIs) play important roles in many molecular processes in the cell. Based protein interaction network analysis (PINA) platform, PPIs network were predicted using proteins of moso bamboo. We provide search a protein or multi-proteins to present its/their network(s).

Firstly,take “PH01000000G1500” as an example.

Then, the result page see the following.

3.3 GBrowse

GBrowse was incorporated in BambooGDB to facilitate viewing the different types of various factors (gene/CDS/mRNA/FL-cDNA/heterozygous SNP/RNA-seq) simultaneously in the context of genomic regions.

3.4 BLAST

To well complement text-based searches for similar genes with sequence-based methods, an interface for more flexibly viewing BLAST-based search was developed. Our BLAST search contained genome, coding sequence, and protein sequence information for Ph. edulis, Oryza sativa and A. thaliana respectively.

Firstly,take one sequence as an example.

Then, the result page see the following.

3.5 BLAST2seq

The “BLAST2seq” tool produces the alignment of two given sequences using BLAST.

Firstly,take two sequences as an example.

Then, the result page see the following.

3.6 Retrieve Sequences

We provide retrieve a segment of DNA sequences around GENE or SCAFFOLD. Selected sequences in whole genome sequence for moso bamboo will be displayed and downloaded. In addition, corresponding reverse sequences will be obtained.

Firstly, take “PH01000000G0240”, “Downstream” and “2000 bp” as an example.

Then, the result page see the following.

3.7 Comparative Genome Search

In a “Comparative genome search” available from tools, we provide searching function to find orthologous genes that are including in one set of genomes and excluding in another set among bamboo related plant species.

Firstly, take “PH01000000G0240” and select “Sorghum bicolor” and “Phyllostachy heterocycla” as an example.

Then, the result page see the following.

4 Documents

We provide some documents to help users to utilize, analyze and understand the data more comprehensively and efficiently.

Take “data analysis” as one example.

5 Download

Most of data in BambooGDB were available via Download part as the following.

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