Entering edit mode
25 days ago
m.ciolek
•
0
Hi,
I try to download 5 interactors for my protein and also their seqences. I do have gene IDs from ensembl. I do not have problem with downloading gene IDs of interactors, but I fail to download their aminoacid seqences. It is very important, because I need this specific transcript that is inteacting with my protein. I can not do it manually, because I have a lot of proteins to analyse.
I tried to use R and package STRINGdb, but I get a lot of 404 error. Same with python script. I can not find informations on forums that would help me. I can use ensembl database and download sequences from there, so it is not a problem with internet connection.
Maybe someone of you tried to do it and succeeded? I appreciate all comments and advice :)
You can download the entire protein set for STRING from https://string-db.org/cgi/download You can filter the data for the organism you are interested in further reducing the size of the download.