Get CDS from WGS fasta OR download just CDS

Question

[moranr]

Hi,

I have many CDS for species genomes I wish to download. I can get 70% with a script. However, there are some I need to get manually and am having trouble finding the coding sequence (CDS) not WGS.

For example, ftp://ftp.ncbi.nih.gov/genomes/Acromyrmex_echinatior has many dirs/files, and I have this entire WGS genome in a fasta file, but don't know how to get the CDS.

Can someone please assist me?

Thanks,
R

Answer 1

[mark.ziemann]

There is a genome annotation file in the GFF folder (ref_Aech_3.9_top_level.gff3) which contains the positional information for genes, mRNAs, exons and CDS. If you use a tool like grep to find all the accessions of the CDS, you can fetch these accession numbers (i.e. gene=LOC105143314) from the rna.fa file.