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Retrieving batch of selected regions sequences from a NCBI db

Hi,

I was wondering if there is any way of downloading a batch of selected regions from sequences from Genbank. I have several accession numbers for different contigs but I need only selected regions from them and not full sequences. Is there any way to download them in a batch and not doing that one by one, because that will take me ages to finish?

sequence ncbi biopython
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written by emilia.skirmuntt • emilia.skirmuntt

Ok, it seems that with Efetch I can still download one sequence fragment at a time (or I'm just missing something, but I was trying for a while now with different options and still no success. I need to download 180 fragments of different contigs and it is getting a bit silly. I was thinking about using Biopython and their Entrez and SeqIO but I got kind of stuck. Input is a file which looks more or less like that:

NW_005871339.1  1   18951   28640
NW_005872753.1  1   4797    13835
NW_005872103.1  1   20997   29747
NW_005878789.1  1   0   5645

What I have so far. But not sure if that even has any chances to work in that form ... 

from Bio import Entrez
from Bio import SeqIO

Entrez.email = "mail'
db = "nuccore"

input = SeqIO.parse('input.fasta', 'r')
output = open('output.fasta', 'w')

handle = Entrez.efetch(db=db, id=input[0], strand=input[1], seq_start=input[2], seq_end=input[3], rettype="fasta", retmode="text")
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written by emilia.skirmuntt • emilia.skirmuntt

Great! Thanks for all your help. It seems I need to improve also my search strategy ;)

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written by emilia.skirmuntt • emilia.skirmuntt

1 answer

Take a look at Entrez programming utilities from NCBI. Example from the link:

Fetch the first 100 bases of the plus strand of GI 21614549 in FASTA format:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=1&seq_start=1&seq_stop=100&rettype=fasta&retmode=text

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written by GenoMax GenoMax

If you have access to NCBI's pre-formatted blast databases you can probably use blastdbcmd to do the same locally with the -range and -entry options.

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written by GenoMax GenoMax

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