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
•
written
by
arronslacey
2 answers
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.
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
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