Genes/feature search can be used to search for genes, CDSs, 16S rRNA, ITS region, pseudogenes, tmRNA and tRNA from various soybean-nodulating Bradyrhizobium accessions available in Bradybase. Available accessions include all 370 field isolates from University of Delaware Bradyrhizobia Culture Collection (UDBCC) and NCBI accessions for Bradyrhizobium spp. reported as soybean root-nodulating, which includes B. diazoefficiens, B. elkanii, B. japonicum, B. huanghuaihaiense, B. yuanmingense, B. ottawaense and B. liaoningense.
1. Search by Name
Gene/Feature Name: Input full or part of gene symbol or annotated name for the gene, CDSs or other features. Search for genes with exact match, contains, starts with or ends with the input provided in the text area. Search is not case sensitive.
File Upload: Upload a set of gene symbols or gene names in a file with each name on different line
2. Search by Organism and Type
Species: Select one or more available soybean root-nodulating Bradyrhizobium spp. to search for genes and features found in each type of species.
Isolate/accession name: Select one or more isolates/accessions names from the box to search for genes/features found in the organism. Users can scroll through the box or type in the search box to get the desired accession names. Accessions are grouped according to the species they belong to. In the accessions, characters after hyphen belong to different species they belong to:
"Bd" => "B. diazoefficiens"
"Be" => "B. elkanii"
"Bj" => "B. japonicum"
"Bh" => "B. huanghuaihaiense"
"By" => "B. yuanmingense"
"Bo" => "B. ottawaense"
"Bl" => "B. liaoningense"
Type: Select one or more feature types from 16S rRNA gene, CDS (Coding Sequence), gene, ITS (Internal Transcribed)region, pseudogene, tRNA and tmRNA (Transfer-messenger RNA)
3. Search by Putative Function
GO Term: Gene Ontology term assigned to a CDS as functional annotation
BLAST Description: Full or part of description of sequences homologous to the CDS
InterPro Description: Functional term assigned to a CDS after InterPro analysis