How to find a ncbi nucleotide entry in the FTP site

Question

[leontp587]

Hello,

I have a big list of ncbi accession numbers for plasmids that I want to grab the sequences to. Examples:

gi|6090378|emb|A78782.1|
gi|154735|gb|K00546.1
gi|1208491|dbj|D45834.1

These are all plasmids, but none of them seem to show up under the ftp://ftp.ncbi.nih.gov/genomes/Plasmids/ folder. Anyone know why?

How can I find these records in the FTP site? I tried to use an FTP program to search for a file with A78782 in its name but this would take days given how big the FTP site is.

Sorry for this very newbie question. I'm completely new to this.

I know it's possible to use e-utils, but I have several tens of thousands of these accession numbers, so FTP would seem faster.

Answer 1

[Neilfws]

To answer "anyone know why" first, take a look at the README in FTP genomes which includes this line:

Plasmids: sequence and annotation of RefSeq plasmids

So only plasmids with RefSeq accessions are found there; you have GenBank accessions.

I'm pretty sure that you will not find a separate GenBank division for plasmid sequences in the FTP site. If you don't want to mirror GenBank locally or use eutils, you could try Batch Entrez, then Send to -> File -> Fasta.

Answer 2

[5heikki]

Your best bet is probably eutils. You can retrieve 500 seqs with every call so even several tens of thousands isn't such a big deal. Here $1 is a list of GIs and Entrez Direct is assumed to be in $PATH:

#!/bin/bash
split -l 500 -a 5 $1 input.
for f in input.*
do
IDs=$(cat $f | tr "\n" ",")
epost -db nuccore -id $IDs | efetch -format fasta > $f.output
done
cat *.output > plasmids.fna
#Everything worked out? rm input.* output.*