Question: Downloading fasta sequence for a PDB entry
0
gravatar for henriquezvera.95
11 months ago by
henriquezvera.950 wrote:

I would like to know if it is possible to download the sequence FASTA of a pdb file using biopython

biopython genome • 388 views
ADD COMMENTlink modified 11 months ago by Sej Modha4.7k • written 11 months ago by henriquezvera.950

[ Please read before posting a question ] -- How To Ask A Good Question - what have you tried so far?

You can use NCBI unix eutils

esearch -db protein -query '1REV[All Fields] AND pdb[filter]'|efetch -format fasta
ADD REPLYlink modified 11 months ago • written 11 months ago by Sej Modha4.7k

There was a post some time ago:

How download a sequence fasta from PDB using biopython / python?

ADD REPLYlink written 11 months ago by natasha.sernova3.7k
0
gravatar for Joe
11 months ago by
Joe17k
United Kingdom
Joe17k wrote:

Kind of a hacky solution (since it downloads the PDB first technically) but here's something you can use as a one-liner:

$ wget -O - https://files.rcsb.org/download/1A80.pdb 2>/dev/null \
   | python -c "import sys; from Bio import SeqIO; SeqIO.convert(sys.stdin, 'pdb-atom', sys.stdout, 'fasta')"
>1A80:A
TVPSIVLNDGNSIPQLGYGVFKVPPADTQRAVEEALEVGYRHIDTAAIYGNEEGVGAAIA
ASGIARDDLFITTKLWNDRHDGDEPAAAIAESLAKLALDQVDLYLVHWPTPAADNYVHAW
EKMIELRAAGLTRSIGVSNHLVPHLERIVAATGVVPAVNQIELHPAYQQREITDWAAAHD
VKIESWGPLGQGKYDLFGAEPVTAAAAAHGKTPAQAVLRWHLQKGFVVFPKSVRRERLEE
NLDVFDFDLTDTEIAAIDAMDPGDGSGRVSAHPDEVD

Just replace 1A80 in the wget link to whatever the PDB ID you're interested in is. BioPython doesn't have the ability to download the data inherently, so you need to pass it the file somehow. I've elected to do this in the shell, but you could also do this natively with python, but its more complicated (IMO).

If you want to save it as a file, stick a redirect to a file at the end of the command:

(previous command)... > pdbsequence.fa
ADD COMMENTlink modified 11 months ago • written 11 months ago by Joe17k
0
gravatar for Sej Modha
11 months ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

ADD COMMENTlink written 11 months ago by Sej Modha4.7k
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