Download gene names and annotations *.gff

Question

[fernan23]

Hello everyone,

I am attempting to assemble some genomes for RNA-seq. The first thing I need to do is have an annotated genome that I can use as a baseline for RNA-seq.

When I use the *.gff file provided by NCBI here

it does not provide the gene product names, it only at best tells me where the CDS are and the genes themselves. I was wondering how and where I could download a *.gff file that has the gene product names also included such as "DNA Polymerase" or "Endonuclease" etc.

I think the file must be in *.gff format since the program I am using DNAStar only gives that type as an option.

Thank you for your efforts and time,

Kind Regards,

DF

Answer 1

[Istvan Albert]

See the Illumina iGenomes

The iGenomes are a collection of sequence and annotation files for commonly analyzed genomes. Each iGenome contains data for one species, downloaded from one source (UCSC, NCBI, or Ensembl), for one genomic build.

See the list here.

[Louis]

NB Cufflinks has moved from umd.edu: see cole-trapnell-lab.github.io/cufflinks/igenome_table/index.html. The official Illumina page for iGenomes (support.illumina.com/sequencing/sequencing_software/igenome.html) has several more species listed.

Answer 2

[fernan23]

Thanks Istvan. Unfortunately the organism I am studying is not listed. Interestingly I looked again and the data is found in the gff file. I guess my question should be refined:

Is there a way to show additional information in the gene features table that is produced by DNAstar program

I can see the product name when i open the file in excel it just doesn't show up in the program. I suppose I should email tech support.

Answer 3

[fernan23]

UPdate:

Worked on it a little more. While I couldn't get gene product names, the genes are now showing up in RNA-seq workflow!

I got it from here, thanks for the suggestions!