Questions tagged [ncbi]

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How to get the nucleotide sequence for protein NCBI accession code, programatically?

It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
Laura's user avatar
  • 777
2 votes
0 answers

How do you go about grabbing proper genotyping infomation from dbSNP using entrez API?

I made an R function to grab rsID genotypes from dbSNP using the entrez API. For example, here is the xml output that I am trying to parse:
Blaze9's user avatar
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How to access specific SRA sequences within an SRP file?

How do you get a specific 100 SRA sequences from a Bioproject which contains 400 runs, when you don't need all of them?
Kirti Kulanthaivel's user avatar
2 votes
2 answers

How do i search by these gene properties in NCBI's GenBank?

I want to search GenBank entries by gene product and taxon id. Taking the 16s rRNA as an example for a gene and Piscirickettsia salmonis (taxon:1238) for a taxon:
Freezing Soul's user avatar
2 votes
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Custom-made kraken2 catalogue

I am looking for instructions on creating a custom-made kraken2 catalogue from the sequences of my choice and the corresponding phylogenetic tree in newick notation. I will appreciate an input on ...
Roger Vadim's user avatar
4 votes
1 answer

What is the NCBI's definition of an "atypical genome"?

Using the new NCBI Datasets platform, you can browse the collection of genomes associated with one or more taxa. For example, searching Pseudomonas aeruginosa returns 19,878 genomes as of 29 March ...
acvill's user avatar
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Kraken2 Standard Database failing to build (unexpected FTP path)

I am attempting to build just the standard Kraken2 Database by using the following command: kraken2-build --standard --threads 24 --db $DBNAME I am returned the ...
InterestingQuestions61's user avatar
2 votes
1 answer

how to do manual search on NCBI with biopython and add link to publication

I'm trying to reproduce a complex manual search on NCBI using BioPython, but obviously something is not right. My command line is not working, but I'd especially like a way to have an accurate search ...
Marine Bergot's user avatar
1 vote
1 answer

How to set Entrez Direct - ESearch NCBI entrez to pipe or ignore errors?

I am using the following one-liner with NCBI entrez to query their databases from the terminal (see Entrez Direct: E-utilities on the Unix Command Line: ...
Sudoh's user avatar
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