Thanks, Uniprot ID converter looks good. As far as I know, 'b0014' etc. are 'ordered locus names', ‘ORF numbers’, ‘CDS numbers’ or ‘Gene numbers’ (http://www.uniprot.org/help/gene_name ). If I choose "gene name" in the first drop down everything appears to work! So thank you!
Batch convert gene numbers (ordered locus names) to protein IDs
I asked the same question on stack exchange.
I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to convert them all to protein IDs.
I know how to do it in a non-batch way, since searching Uniprot for 'b0014' returns what (I think) is a protein ID. However I'd like an automated solution, since I might need to repeat this in the future and manually searching even 1000 would take forever.
1 answer
Uniprot ID converter tool is generally the best way of mapping names in bulk. Are the b* numbers STRING ID's? If I select STRING as the source they are not mapping to Uniprot.
Log in to answer this question.
More posts like this
-
Protein to gene name conversion
written by mm2568 •
-
How to perform GO enrichment analysis on sRNA-seq
written by jomagrax •
-
Conversion of Ensembl Gene Ids to Uniprot Ids
written by deddu •
-
How to find KO number for each protein represented by STRING ID?
written by larcwind •
-
Most efficient strategy to convert from Ensembl protein IDs (ENSP) to Entrez Gene Symbols?
written by sam237337
-
Bulk download of gene names NCBI
written by T_18 •
-
Advice needed for GO enrichment
written by dankwc2000 •
-
Extracting loci index from uniprot with high confidence
written by olle.nordesjo •
-
Uniprotkb And Genes
written by willyjensen •
-
Options For Automatically Retrieving Entrez Gene Names From Id?
written by Matt LaFave
Please do not cross-post.