Question: How do I download entire human genome for local blast formatting and searching?
0
gravatar for b10hazard
2.2 years ago by
b10hazard0
b10hazard0 wrote:

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?

blast ncbi • 1.5k views
ADD COMMENTlink written 2.2 years ago by b10hazard0
2

Do I download the fasta files for all 22 chromosomes, the X chromosome, and then the Y chromosome and concatenate them?

yes

see also Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Pierre Lindenbaum121k
1
gravatar for genomax
2.2 years ago by
genomax69k
United States
genomax69k wrote:

You can get the individual chromosome files from the FTP link you posted above (*ref*fa* files) and then cat the files together or get the entire genome in a single file from UCSC here.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax69k
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