Question: How do I download entire human genome for local blast formatting and searching?
0
gravatar for b10hazard
22 months 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 • 1.2k views
ADD COMMENTlink written 22 months 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 22 months ago • written 22 months ago by Pierre Lindenbaum118k
1
gravatar for genomax
22 months ago by
genomax64k
United States
genomax64k 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 22 months ago • written 22 months ago by genomax64k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1876 users visited in the last hour