Tutorial of MBKBase


1. Brief introduction

2. Search genes by Name

3. Search genes and SNPs by genomic regions

4. Search germplasm by name

5. Search phenotype by name


1. Brief introduction  top

MBKBase is a database that contains 25,440,486,885 Single Nucleotide Polymorphisms (SNPs) and 2,897,225,156 insertions or deletions (INDELs) of 3,899 rice cultivars all over the world. Three types of gene annotation are included in the database. (MSU, IRGSP and IGDB).

Users can search SNPs and genes by genomic regions or search genes by gene id or gene name. Users can also search for germplasm and phenotype by their name respectively. GBrowse and blast are integrated to the website for genome data visualization and user-defined query support towards the target reference genomes.

You can visit MBKBase by entering its address http://mbkbase.org/

Background of data collection, processing and evaluation could be found in Notes and Data page


2. Search genes by Name  top

In the “Genotype” page, the form for searching gene by name can be found on the top. Users can identify a gene by id (such as MSU locus identifier, IRGSP/RAP2 locus ID) or gene name (such as “PYRICULARIA ORYZAE RESISTANCE 5”).

The search result can lead to gene summary page that contains detailed gene information including gene structure, annotation, SNPs, INDELs, haplotypes and paralogous genes. A gbrowse link of a gene can also be found at the gene summary page.


3. Search genes and SNPs by genomic regions  top

In the “Genotype” page, the form for searching genes and SNPs by genomic regions can be found in the middle. Users can specify a chromosome and input a range.

The search result of genes can lead to gene summary page.

The result of SNPs shows position of the SNP, the reference genotype, the different SNP types among different samples, the major allele in cultivars and the frequency of major allele, the transcripts in which the SNP is present, effect (description of SNP), substitution type and codon changes.


4. Search germplasm by name  top

Users can search germplasms by giving a name in the search form which can be found on the “Germplasm” page. It’s better to search in Chinese. But we also add English translation as more germplasms as we can, or Hanyu Pinyin is used as English name for search.

The result can lead to a germplasm summary page, which gives detailed information of a germplasm.


5. Search phenotype by name  top

Users can search phenotypes by giving a name in the search form which can be found on the “Phenotype” page. Only Chinese words can return meaningful result at this moment in time.

Trait summary page links in given to each searched phenotype result.