I have a list of protein IDs from uniprot that was created after blasting a fasta file locally against the uniprot database. I want to convert these IDs to description of the actual proteins. I have tried a few tools, but none seem to do what Uniprots retrieve ID/ mapping do. The only reason I am not using it is because it fails on the large file of genes I have. ANy recommendations on packages or scripts to manage this task would be helpful.
How many identifiers does your list contain? Have you considered splitting it up into lists of about 20000 identifiers each, before submitting it to the UniProt batch retrieve tool?
Please don't hesitate to contact the UniProt helpdesk with more information on the type of data you are submitting, and we'd be happy to advise.