How to download annotation file from ncbi

Overview Publications Citation policy Use and license. Downloads Download Annotations. Overview The gene association files ingested from GO Consortium members are shown in the table below. Filtered Files These files are taxon-specific and reflect the work of specific projects, primarily the model organisms database groups, to provide comprehensive, non-redundant annotation files for their organism.

Dictyostelium discoideum dictyBase dictyBase. Mus musculus Mouse Genome Informatics mgi. Aspergillus nidulans Aspergillus Genome Database aspgd. XML to gff convertion should be fairly easy, but I do not know a tool yet. John, I'm running into the same problem that you had. Were you able to convert the. I'd be interested to hear the best method you found for generating the annotation file that corresponds to the most recent S.

Thanks in advance, jjw. I was not able to figure out how to convert any of the NCBI annotation data into a usable form. I sent an email to NCBI but didn't get a useful reply from them. Thankfully another group has generated a good gene build for Sscr If you can wait that long that would be another good alternative to NCBI's annotation. Thanks for the quick reply, John. No doubt, you've saved me a lot of frustration.

I appreciate it. Location: Dundee, Scotland, UK. There are some convenient tools available that may help in some situations depending on our needs. For searching by taxonomy and downloading genomes assemblies , kaiblin and some others have put together a great tool called ncbi-genome-download , and they have one for downloading individual sequences by accession called ncbi-acc-download.

But like a lot of things, once I had a little familiarity with it, I started to appreciate how useful and powerful it can be. But I still have trouble finding examples when I need them and I always need them when using this. And I often end up digging through several of my old log files to find things, so…. NOTE: This stuff can look messy, mostly because it is; it scares me too.

This page assumes you already have some familiarity with working at the command line. For a while, this was also kind of a huge pain to install on some systems. Start at the Ensembl Fungi page 2.

Click on View full list of all Ensembl Fungi species 3. In [2]:. In [3]:. In [5]:. In [6]:. In [7]:. In [8]:.