The protein, cDNA, and transcript information such as the IDs, aliases, descriptions, lengths and sequences were extracted from the FASTA files and the GFF3 files obtained from the MSU website and MSU genome browser, then converted to tables using perl scripts.
Further, protein, cDNA, and un-spliced mRNA have their own IDs and aliases that were used in MSU V6.1.
A closer look into these cases revealed that redundant Ensembl IDs represented either pseudo-genes or alias IDs.
The search page (http://dailab.sysu.edu.cn/bgdb/database.php) provides an interface for searching the BGDB database with several keywords such as gene symbol, gene alias, reference sequence ID or UniProt ID.
Gene symbol, aliases, gene ID, gene name and reference PubMed ID are reported for each gene.
Gene information section displays NCBI ID, official symbol, description, aliases, Entrez-summary, chromosomal location, orientation, size, sequence and OMIM IDs.
The information included the NCBI gene id, official gene symbol, aliases, gene sequence, gene summary, chromosomal location, potential promoter sequence [-1000 [-10000 bp] and all toanscript sequences (along with exon-intron details) corresponding to each gene.
The output showed the detailed information of gene query for both human and mouse; for instance, the official full name and other aliases, gene ID, OMIM ID and related disease/phenotype, the list of transcript isoforms and their genomic positions, associated KEGG pathway and Gene Ontology.
Currently, supported IDs are Gene Symbols, aliases, Affymetrix probe IDs, Entrez Gene IDs, Refseq, Ensemble, Mouse Genome Database, Rat Genome Database and VEGA IDs.
Gene information was downloaded from the NCBI repository as the dictionary to map the gene IDs, gene symbols and their alias and synonyms.
