I am trying to find the total number of genomes available in the genome database on NCBI using E-utilities. I see just from using the website that there are 39,625 when browsing by organism. I'd just like to pull this number using E-utilities. I've used the following code in Mac Terminal, but it returned only 6314 results. curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=genome&term=overview&rettype=count"
Any ideas how I can edit that code to return the full list of genome IDs?
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emartin.morgan •
Take a look at output of
$ einfo -db genome
$ einfo -db genome | xtract -pattern DbInfo -element Name -element TermCount
ALL UID FILT ORGN PID PRJA PRJT DFLN DSCR STAT AID AACC ANAM GI ACCN RNAM PACC PROT PGI GNID GENE LTAG WGSP PMID BIOP PCID PROP CDT STRN HOST genome_assembly genome_bioproject genome_gene genome_nuccore genome_nuccore_samespecies genome_protein genome_proteinclusters genome_pubmed genome_taxonomy
5674172 0 18 393432 81030 81015 21 40408 27281 4 191288 191288 196002 395879 872215 10882 00 0 0 3027959 0 314634 28232 0 61 9 5807 161224 34
You can parse the following two files to get all sorts of information.
Assembly summary file for GenBank can be found here.
Similar file for RefSeq genomes is here.
NCBI's Genome reports: ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/
Thanks - I found that number too using: curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=genome"
Any idea why these don't match? Sorry if these are very basic questions, I'm extremely new to this and just starting grad school for Biomedical Informatics.
Genomes are in various stages of completion and as a result they may be listed in different sections. The total number shown may include sequences, maps, chromosomes, assemblies, and annotations
If you are only interested in complete genomes then you could parse the genome reports files as shown here: A: most sequenced genomes
Okay, I was thinking it was due to any that might be incomplete. Appreciate the help, but I'm not familiar with that language you're using. Is it Perl? Sorry I'm hopeless! Really just trying to understand how to work within terminal using the specific e-utilities.
It is a command line tool made available by NCBI called unix utilities. You can read more about it here. You can also get similar functionality by NCBI eutils a web interface.
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