get protein sequence from ID

Question

[arronslacey]

Hi - could someone point me to a database that I could query to find the protein sequence when given a protein ID (i.e P51811). I'm familiar with doing some queries on the UCSC server, but there are so many tables!

Thanks very much.

ANSWER

Thanks you to @themysticgeek and @Emily_Ensembl for pointing the uniprot REST API - I had forgotten. On this recomendation I botched this little bash script together to get the sequences from a list of IDs. Hope it helps anyone (feel free to optimize the code if you want!)

#!/bin/bash

#download fasta seqs given file of uniprot ids

file=$1
name=$2

list=$(cat ${1})

mkdir ${name}
cp ${2} ${name}
cd ${name}

for word in ${list}
do
    wget -nv http://www.uniprot.org/uniprot/$word.fasta
done

Answer 1

[kautilya]

P51811 is a Uniprot ID . In order to get its sequence you can simple use the URL http://www.uniprot.org/uniprot/YOUR_PROTEIN_ID.fasta

e.g http://www.uniprot.org/uniprot/P51811.fasta

Besides this there are a large number of other ways to access the sequence - the details of these can be found at the Uniprot REST guide.

Answer 2

[Emily]

Have you tried putting your IDs into the search box in Uniprot?

Alternatively, if you have a long list of them that you want sequences for and they're all Uniprot IDs like this one, you could try BioMart. There's a help video to get you started here. Use:

Database, Ensembl genes

Filters, ID list limit, pick Uniprot from the dropdown and paste in your list

Attributes, Sequences, protein sequences