Where Can I Download Nucleotide Sequences Of Bacterial Genes?

Question

[Tianyang Li]

Hi,

I'd like to get download a large collection of bacterial genes' nucleotide sequences. I'm not sure where to download it.

Can somebody suggest a place that I can download a large collection, maybe a database, of baceterial genes' nucleotide sequences?

I'd like to avoid using a web API to get the sequences one by one.

Thanks!

Answer 1

[Neilfws]

NCBI FTP site for bacterial genomes. The files with gene nucleotide sequence end in .ffn. Note that NCBI include Archaea under the Bacteria directory.

Use something like wget, or mget within FTP to grab the whole collection (or a portion of it; it's quite large).

[Tianyang Li]

I'd like to download individual sequences of genes, I'm not sure if this is available.

[Neilfws]

Then you want the NCBI EUtils API. Also you should rephrase your question; neither "download a large collection" nor "avoid using a web API to get the sequences one by one" indicate that you wanted individual sequences.

Answer 2

[fransua]

hi, you can try here http://bacteria.ensembl.org/index.html and with the biomart tool from there download your CDS.

[Danstaines]

You can either use the Ensembl API, or the BioMart tool, or you can download FASTA dumps containing individual CDS/pep sequence from ftp://ftp.ensemblgenomes.org/pub/current/bacteria/fasta/ e.g. ftp://ftp.ensemblgenomes.org/pub/current/bacteria/fasta/bacillus_collection/b_amyloliquefaciens/cdna/B_amyloliquefaciens.EB1_b_amyloliquefaciens.12.cdna.all.fa.gz

[Tianyang Li]

Thanks, do you know if there's an API that I can use? I'd like to download all the CDS.