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Questions - ncbi

Grab specific values from columns with disordered rows

As the consequence of a misformatted file (which is unfortunately the only file available) I have a few thousand columns each with 9 rows of data in them. Unfortunately, the actual values are in a dif...
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katet

r

ncbi

Votes: 0

Answers: 1

Latest Answer

How about this: dat <- structure(list(`header 1` = c("Parent=gene-SAS_RS00035", "gbkey=CDS", "inference=COORDINATES: similar to AA s...
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DaveArmstrong

How do I provide my Identity / Email when connecting to NCBI through Rentrez?

My project head is telling me that its unacceptable to connect with NCBI to retrieve sequence entries without sending along identifying information such as our institution email. They claim this means...
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BioInfoMan28

r

bioinformatics

ncbi

rentrez

Votes: 0

Answers: 1

Latest Answer

It seems like you need an API key. You can get one from your NCBI account interactively, and it needs to be specified in your .bash_profile (at least on a mac, using bash, not sure your OS / terminal ...
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Nick

How to write a Python code for downloading an abstract from PubMed?

This is the code I have as of now and I have tried multiple different ways to get the correct code but to no avail. I am using the Biopython module for this. from Bio.Entrez import efetch def print_a...
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sonu

python-3.x

download

pubmed

ncbi

Votes: 0

Answers: 1

Latest Answer

Step 1: When using python3, use print() as such: from Bio.Entrez import efetch def print_abstract(pmid): handle = efetch(db='pubmed', id=pmid, retmode='text', rettype='abstract') print(handl...
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melvio

NCBI Blast API use QuickBLASTP program

I'm using NCBI Blast's web API. In their browser-based Blast search, they offer a program called QuickBLASTP which is immensely faster than the regular blastp. How can I use this program inside of the...
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Ayush

python

blast

ncbi

Votes: 0

Answers: 0

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