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I'm trying to make a copy of the entire human genome for local blast queries on my machine. I understand that I need to download it from the NCBI FTP server here...

ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens

After downloading it I need to format it into a database that blast can search. I do this using NCBI's makeformatdb command. It is run like this...

makeblastdb -in entire_human_genome.fasta -dbtype nucl -title human_genome -out human_genome.db

My question is... Where do I get the fasta file containing the entire human genome? Do I download the fasta files for all 22 chromosomes, the X chromosome, and then the Y chromosome and concatenate them? Is there a fasta file on the site containing the entire genome? A fasta file that is not partitioned by chromosome?

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You can either download and concatenate the individual chromosomes from NCBI or make your life easier and download a single fasta file from Gencode (note that that's the primary assembly, if you want the one with haplotypes then it's here).

Having written all of that, the "human_genomic" files on the NCBI FTP server are the prebuilt blast databases for humans.

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  • $\begingroup$ Just had a look at the prebuilt blast databases you linked to. I would want the one named "human_genomic_transcript.tar.gz". That is the largest one at 6.0 GB. Is this the complete genome? $\endgroup$
    – b10hazard
    May 10, 2017 at 19:17
  • $\begingroup$ You probably want the 21 human_genomic.??.tar.gz files. They each contain subsets of the whole database. The human_genomic_transcript.tar.gz file is a superset of that, additionally containing refseq transcripts. See more details here. $\endgroup$
    – Devon Ryan
    May 10, 2017 at 21:20

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