Download human gene sequences

[ritzriya]

Hi all,

I have been searching NCBI as well as UCSC and Ensembl. This is really getting weird but I want to download all the Genes for humans in FASTA format. I am unable to get this from any of these sites. Can anyone please help?

[NicoBxl]

I think it's possible via biomart : http://www.ensembl.org/biomart/martv...96b8021ee85098

[ritzriya]

I think it's possible via biomart : http://www.ensembl.org/biomart/martv...96b8021ee85098

Thank you NicoBxl. But these sequences are in the amino acid format. I wanted it in the form of ATGC otherwise I could have got it from UniProtKB. I need to carry out the alignment using the gene sequences in ATGC sequence FASTA format.

It would be of great help if you could guide.

[ttnguyen]

I think Galaxy can help http://main.g2.bx.psu.edu/

In Galaxy you can retrieve all the genes from UCSC GB then fetch the DNA sequence of the genes in FASTA format.

[ulz_peter]

You could as well download the Fasta Files of the FTP-server of UCSC:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

There is a mRNA.fa and a refMrna entry for the human hg19 genome. Data from earlier assemblies are available as well.

[iansealy]

And for Ensembl:

http://www.ensembl.org/info/data/ftp/index.html

[kmcarr]

And to complete the list, NCBI RefSeq:

ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/