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Update download-go-annotations.md
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suzialeksander authored Jul 24, 2024
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Expand Up @@ -50,13 +50,13 @@ For all other organisms we recommend downloading annotations from one of the fol
* [NCBI RefSeq](https://ftp.ncbi.nlm.nih.gov/genomes/refseq/){:target="blank"}: If your organism has a reference genome assembly in NCBI, GO annotations are available in GAF format through NCBI Gene identifiers. Annotation files are available for all eukaryotic genomes available at NCBI RefSeq. Note that GO annotations are not currently available for archaea, bacteria or viruses.
* Start at the [NCBI homepage](https://www.ncbi.nlm.nih.gov/){:target="blank"}
* Enter your organism in the search box near the top of the page and click Search, e.g. [Anopheles gambiae](https://www.ncbi.nlm.nih.gov/search/all/?term=Anopheles%20gambiae){:target="blank"}
<br><img src="/assets/NCBIsearchbox.png" alt="NCBI homepage search" width="600" div style="border: 2px solid black;"/></div><br>
<br><img src="/assets/NCBIsearchbox.png" alt="NCBI homepage search" width="600" div style="border: 2px solid black;"/><br>
* Follow the ["Genomes" link](https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=7165){:target="blank"}
<br><img src="/assets/NCBIgenomelink.png" alt="NCBI Genomes link" width="600"/><br>
<br><img src="/assets/NCBIgenomelink.png" alt="NCBI Genomes link" width="600" div style="border: 2px solid black;"/><br>
* Select the [reference assembly](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_943734735.2/){:target="blank"} at the top of the list; this entry is indicated with a green "reference genome" icon and a GCF identifer listed in the RefSeq column
<br><img src="/assets/NCBIrefgenome.png" alt="NCBI reference assembly" width="600"/><br>
<br><img src="/assets/NCBIrefgenome.png" alt="NCBI reference assembly" width="600" div style="border: 2px solid black;"/><br>
* Click on the [FTP link](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/943/734/735/GCF_943734735.2_idAnoGambNW_F1_1/){:target="blank"}
<br><img src="/assets/NCBIftp.png" alt="NCBI FTP link to GAF" width="600"/><<br>
<br><img src="/assets/NCBIftp.png" alt="NCBI FTP link to GAF" width="600" div style="border: 2px solid black;"/><br>
* Download the file with the suffix `gene_ontology.gaf.gz`, e.g. `GCF_943734735.2-RS_2023_12_gene_ontology.gaf.gz`

### 3. If you cannot find annotations for your organism for download as described above
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