BioMart Convert IDs
BioMart is a very handy tool when you want to convert IDs from different databases. The following is a list of 20 IDs of wheat proteins from the NCBI RefSeq database:
NP_114254.1 NP_114277.1 NP_114275.1 NP_114283.1 YP_398395.1 NP_114279.1 NP_114274.1 NP_114273.1 NP_114273.1 NP_114265.1 NP_114247.1 NP_114243.1 NP_114276.1 NP_114276.1 NP_114262.1 NP_114287.1 NP_114239.1 NP_114276.1 NP_114243.1 NP_114280.1
Generate a list that shows to which Ensembl Gene IDs and to which gene names these RefSeq IDs correspond. Do these 20 transcripts correspond to 20 genes?
Click New. Choose the Ensembl Plants Genes database. Choose the Triticum aestivum genes dataset.
Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input external references ID list - RefSeq peptide ID(s) and enter the list of IDs in the text box (either comma separated or as a list). HINT: You may have to scroll down the menu to see these.
Count shows 68 genes (the hybridisations and whole genome duplications in wheat’s evolutionary history means that many RefSeqs are duplicated across the genome)..
Click on Attributes in the left panel. Select the Features attributes page. Expand the Gene section by clicking on the + box. Select Gene name from the Gene section. Expand the External section by clicking on the + box. Select RefSeq Peptide ID from the External References section.
Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.
