FlyBase:Using FTP Archives
| Important Notice |
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| We recently moved our files out of the FTP server where they were housed because that server was a major target of bot scraping. They are now in a S3 FTP file storage area, but we have tried to emulate most FTP functions. Please contact us via the Contact FlyBase form if you are experiencing issues. Some archives are not available while we complete this process. 30 Jun 2025. |
Genomes archives
Sequence information for other Drosophila species is no longer provided by FlyBase. Gene model annotations for this species are now updated and maintained at NCBI, using the gnomon automated annotation pipeline. See the Eukaryotic genomes annotated at NCBI page.
The genomes Drosophila_melanogaster folder holds genomic sequence data from selected releases.
Data includes sequences in FASTA, GFF, and GTF file formats, as well as the Chado-XML database files for that species and release. The dna/ folders contain unprocessed sequences as .raw scaffold files.
Archive of selected releases
The Index of releases folder holds data for selected releases for D. melanogaster. These folders include:
- a chado-XML/ folder, containing the Chado-XML database files
- a collaborators/ folder, containing packages of data that we provide to other biological databases
- a precomputed_files/ folder, containing precomputed files, which are plaintext tab-separated files that provide helpful intersections of FlyBase data types (e.g., fbal_to_fbgn_fb_*.tsv which lists all alleles associated with all genes). Where * denotes the release.
- a psql/ folder, continaing compressed SQL files of the Chado database
Most queries, whether via with QuickSearch and a HitList, Batch Download, or Vocabularies are filtering information found in one of the Precomputed Files. Using the information in our wiki, you will hopefully be able to find a file that meets your needs.
You may need to do further filtering on these files, as they are large. Importing them as plain text into a spreadsheet program is a convenient way to search in them. Once the data is imported, you can use Find/searching, column sorting and filtering, or a pivot table to find the lines in that table containing your information of interest.