get the uniprot accession from ensembl protein ID

Question

[Moses]

Hi,

I have a list of Ensembl protein pairs(homologs) with their respective ensembl protein IDs. I want to find a way to convert these Ensembl protein IDs to Uniprot IDs. for example given: ENSP00000361930 I want to get: 1433B_HUMAN

Is there a function in biopython that does this conversion? I really need to script it because the list is huge and I cant do it manually.

Thank you

Answer 1

[Pierre Lindenbaum]

use uniprot ID mapping http://www.uniprot.org/uploadlists/

[Moses]

well I thought about that but whenever I give a file with list of ensembl protein IDs for example:

ENSP00000379287
ENSG00000166913
ENSP00000355042
ENSP00000379287
ENSP00000379287

then its giving me fasta files as outputs with protein sequences accession numbers and other information that I do not need

>tr|A0A0J9YWE8|A0A0J9YWE8_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=4 SV=1
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLFFRMPHSKTTLRKYCSVYEA
WTPSELLLLSCWTNILFPMLHNQKVRCST
>tr|A0A0J9YWZ2|A0A0J9YWZ2_HUMAN 14-3-3 protein beta/alpha (Fragment) OS=Homo sapiens GN=YWHAB PE=4 SV=1
XAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYR
EKIEAELQDICNDVLVHLVFR
>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN
>sp|P31946-2|1433B_HUMAN Isoform Short of 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB
MDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWR
VISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLK
MKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYE
ILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAG
EGEN
>tr|Q4VY19|Q4VY19_HUMAN 14-3-3 protein beta/alpha (Fragment) OS=Homo sapiens GN=YWHAB PE=1 SV=1
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVL
>tr|Q4VY20|Q4VY20_HUMAN 14-3-3 protein beta/alpha (Fragment) OS=Homo sapiens GN=YWHAB PE=1 SV=1
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERN

for example. Is there a way to just get the protein ID rather than all this info?

[Pierre Lindenbaum]

button "Download" -> Format: "Mapping Table"

Answer 2

[Laura Luebbert]

gget info!! https://github.com/pachterlab/gget

[Andrzej Zielezinski]

Perfect! Why am I just hearing about this now? :)