Precomputed data files for the current release

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Main Data Set
Postgres Chado Database Dump
	Chado database (ftp://ftp.flybase.net/releases/FB2013_03/psql)
Drosophila Data
	Current FTP repository (ftp://ftp.flybase.net/releases/FB2013_03/) Current Chado-XML repository (ftp://ftp.flybase.net/releases/FB2013_03/chado-xml) Current Reporting-XML repository (ftp://ftp.flybase.net/releases/FB2013_03/reporting-xml) Genomes FTP archive (ftp://ftp.flybase.net/genomes/)
Synonyms
Item Chado XML Reporting XML Other FlyBase Synonyms fb_synonym_fb_2013_03.tsv.gz
Genes
Item Chado XML Reporting XML Other Genes data download download RNA-Seq RPKM values gene_rpkm_report_fb_2013_03.tsv.gz Physical Interaction table physical_interactions_fb_2013_03.tsv.gz FBgn ⇔ DB Accession IDs fbgn_NAseq_Uniprot_fb_2013_03.tsv.gz FBgn ⇔ Annotation ID fbgn_annotation_ID_fb_2013_03.tsv.gz FBgn ⇔ GLEANR IDs fbgn_gleanr_fb_2013_03.tsv.gz FBgn ⇔ FBtr ⇔ FBpp IDs fbgn_fbtr_fbpp_fb_2013_03.tsv.gz FBgn Exons ⇔ Affy1 fbgn_exons2affy1_overlaps.tsv.gz FBgn Exons ⇔ Affy2 fbgn_exons2affy2_overlaps.tsv.gz Genes GO data gene_association.fb.gz Genes map table gene_map_table_fb_2013_03.tsv.gz Gene summaries gene_summaries.tsv.gz Orthologs gene_orthologs_fb_2013_03.tsv.gz Unique Protein Isoforms dmel_unique_protein_isoforms_fb_2013_03.tsv.gz
Alleles and Stocks
Item Chado XML Reporting XML Other Allele data download download Stock data download download stocks_FB2013_03.tsv.gz Genetic Interactions allele_genetic_interactions_fb_2013_03.tsv.gz Phenotypic data allele_phenotypic_data_fb_2013_03.tsv.gz
Nomenclature
Item Chado XML Reporting XML Other Species abbreviation list species.ab.gz
Ontology Terms
Frozen Files used for this release of FlyBase
Item Chado XML Reporting XML Other FBbt: (fly_anatomy) fly_anatomy.obo.gz FBdv: (fly_development) fly_development.obo.gz FBcv: (controlled vocab) flybase_controlled_vocabulary.obo.gz FBsv: (stock ontology) flybase_stock_vocabulary.obo.gz GO: (gene ontology) gene_ontology.obo.gz FBbi: (image ontology) image.obo.gz SO: (sequence ontology) so.obo.gz
Current 'Live' Files
Item Chado XML Reporting XML Other FBbt: (fly_anatomy) fly_anatomy.obo FBdv: (fly_development) fly_development.obo FBcv: (controlled vocab) flybase_controlled_vocabulary.obo GO: (gene ontology) gene_ontology.obo FBbi: (image ontology) image.obo SO: (sequence ontology) so.obo
Genomes: Annotation and Sequence
All Sequenced Drosophila Species
	Current FTP repository (ftp://ftp.flybase.net/releases/FB2013_03/) FTP archive (ftp://ftp.flybase.net/genomes/) Release notes
Drosophila melanogaster (Dmel)
	Current Dmel FTP repository (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/) Current Dmel FastA FTP repository (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/) Current Dmel GFF repository (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/) Dmel FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/)
FASTA
	dmel-all-aligned-r5.51.fasta.gz dmel-all-CDS-r5.51.fasta.gz dmel-all-chromosome-r5.51.fasta.gz dmel-all-clones-r5.51.fasta.gz dmel-all-exon-r5.51.fasta.gz dmel-all-five_prime_UTR-r5.51.fasta.gz dmel-all-gene_extended2000-r5.51.fasta.gz dmel-all-gene-r5.51.fasta.gz dmel-all-intergenic-r5.51.fasta.gz dmel-all-intron-r5.51.fasta.gz dmel-all-miRNA-r5.51.fasta.gz dmel-all-miscRNA-r5.51.fasta.gz dmel-all-ncRNA-r5.51.fasta.gz dmel-all-predicted-r5.51.fasta.gz dmel-all-pseudogene-r5.51.fasta.gz dmel-all-sequence_features-r5.51.fasta.gz dmel-all-synteny-r5.51.fasta.gz dmel-all-three_prime_UTR-r5.51.fasta.gz dmel-all-transcript-r5.51.fasta.gz dmel-all-translation-r5.51.fasta.gz dmel-all-transposon-r5.51.fasta.gz dmel-all-tRNA-r5.51.fasta.gz
GFF
	dmel-all-r5.51.gff.gz dmel-all-no-analysis-r5.51.gff.gz
Drosophila ananassae (Dana)
	Current Dana FTP repository (ftp://flybase.net/genomes/Drosophila_ananassae/current/) Current Dana FTP FastA repository (ftp://flybase.net/genomes/Drosophila_ananassae/current/fasta/) Current Dana GFF repository (ftp://flybase.net/genomes/Drosophila_ananassae/current/gff/) Dana FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_ananassae/)
FASTA
	dana-all-CDS-r1.3.fasta.gz dana-all-chromosome-r1.3.fasta.gz dana-all-exon-r1.3.fasta.gz dana-all-gene_extended2000-r1.3.fasta.gz dana-all-gene-r1.3.fasta.gz dana-all-intergenic-r1.3.fasta.gz dana-all-intron-r1.3.fasta.gz dana-all-predicted-r1.3.fasta.gz dana-all-transcript-r1.3.fasta.gz dana-all-translation-r1.3.fasta.gz
GFF
	dana-all-r1.3.gff.gz dana-gff_all_scaffolds-r1.3.tar.gz
Drosophila erecta (Dere)
	Current Dere FTP repository (ftp://flybase.net/genomes/Drosophila_erecta/current/) Current Dere FTP FastA repository (ftp://flybase.net/genomes/Drosophila_erecta/current/fasta/) Current Dere GFF repository (ftp://flybase.net/genomes/Drosophila_erecta/current/gff/) Dere FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_erecta/)
FASTA
	dere-all-CDS-r1.3.fasta.gz dere-all-chromosome-r1.3.fasta.gz dere-all-exon-r1.3.fasta.gz dere-all-gene_extended2000-r1.3.fasta.gz dere-all-gene-r1.3.fasta.gz dere-all-intergenic-r1.3.fasta.gz dere-all-intron-r1.3.fasta.gz dere-all-predicted-r1.3.fasta.gz dere-all-transcript-r1.3.fasta.gz dere-all-translation-r1.3.fasta.gz
GFF
	dere-all-r1.3.gff.gz dere-gff_all_scaffolds-r1.3.tar.gz
Drosophila grimshawi (Dgri)
	Current Dgri FTP repository (ftp://flybase.net/genomes/Drosophila_grimshawi/current/) Current Dgri FTP FastA repository (ftp://flybase.net/genomes/Drosophila_grimshawi/current/fasta/) Current Dgri GFF repository (ftp://flybase.net/genomes/Drosophila_grimshawi/current/gff/) Dgri FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/)
FASTA
	dgri-all-CDS-r1.3.fasta.gz dgri-all-chromosome-r1.3.fasta.gz dgri-all-exon-r1.3.fasta.gz dgri-all-gene_extended2000-r1.3.fasta.gz dgri-all-gene-r1.3.fasta.gz dgri-all-intergenic-r1.3.fasta.gz dgri-all-intron-r1.3.fasta.gz dgri-all-predicted-r1.3.fasta.gz dgri-all-transcript-r1.3.fasta.gz dgri-all-translation-r1.3.fasta.gz
GFF
	dgri-all-r1.3.gff.gz dgri-gff_all_scaffolds-r1.3.tar.gz
Drosophila mojavensis (Dmoj)
	Current Dmoj FTP repository (ftp://flybase.net/genomes/Drosophila_mojavensis/current/) Current Dmoj FTP FastA repository (ftp://flybase.net/genomes/Drosophila_mojavensis/current/fasta/) Current Dmoj GFF repository (ftp://flybase.net/genomes/Drosophila_mojavensis/current/gff/) Dmoj FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_mojavensis/)
FASTA
	dmoj-all-CDS-r1.3.fasta.gz dmoj-all-chromosome-r1.3.fasta.gz dmoj-all-exon-r1.3.fasta.gz dmoj-all-gene_extended2000-r1.3.fasta.gz dmoj-all-gene-r1.3.fasta.gz dmoj-all-intergenic-r1.3.fasta.gz dmoj-all-intron-r1.3.fasta.gz dmoj-all-predicted-r1.3.fasta.gz dmoj-all-transcript-r1.3.fasta.gz dmoj-all-translation-r1.3.fasta.gz
GFF
	dmoj-all-r1.3.gff.gz dmoj-gff_all_scaffolds-r1.3.tar.gz
Drosophila persimilis (Dper)
	Current Dper FTP repository (ftp://flybase.net/genomes/Drosophila_persimilis/current/) Current Dper FTP FastA repository (ftp://flybase.net/genomes/Drosophila_persimilis/current/fasta/) Current Dper GFF repository (ftp://flybase.net/genomes/Drosophila_persimilis/current/gff/) Dper FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_persimilis/)
FASTA
	dper-all-CDS-r1.3.fasta.gz dper-all-chromosome-r1.3.fasta.gz dper-all-exon-r1.3.fasta.gz dper-all-gene_extended2000-r1.3.fasta.gz dper-all-gene-r1.3.fasta.gz dper-all-intergenic-r1.3.fasta.gz dper-all-intron-r1.3.fasta.gz dper-all-predicted-r1.3.fasta.gz dper-all-transcript-r1.3.fasta.gz dper-all-translation-r1.3.fasta.gz
GFF
	dper-all-r1.3.gff.gz dper-gff_all_scaffolds-r1.3.tar.gz
Drosophila pseudoobscura pseudoobscura (Dpse)
	Current Dpse FTP repository (ftp://flybase.net/genomes/Drosophila_pseudoobscura/current/) Current Dpse FTP FastA repository (ftp://flybase.net/genomes/Drosophila_pseudoobscura/current/fasta/) Current Dpse GFF repository (ftp://flybase.net/genomes/Drosophila_pseudoobscura/current/gff/) Dpse FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/)
FASTA
	dpse-all-CDS-r3.1.fasta.gz dpse-all-chromosome-r3.1.fasta.gz dpse-all-exon-r3.1.fasta.gz dpse-all-gene_extended2000-r3.1.fasta.gz dpse-all-gene-r3.1.fasta.gz dpse-all-intergenic-r3.1.fasta.gz dpse-all-intron-r3.1.fasta.gz dpse-all-predicted-r3.1.fasta.gz dpse-all-synteny-r3.1.fasta.gz dpse-all-transcript-r3.1.fasta.gz dpse-all-translation-r3.1.fasta.gz
GFF
	dpse-all-r3.1.gff.gz dpse-gff_all_scaffolds-r3.1.tar.gz
Drosophila sechellia (Dsec)
	Current Dsec FTP repository (ftp://flybase.net/genomes/Drosophila_sechellia/current/) Current Dsec FTP FastA repository (ftp://flybase.net/genomes/Drosophila_sechellia/current/fasta/) Current Dsec GFF repository (ftp://flybase.net/genomes/Drosophila_sechellia/current/gff/) Dsec FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_sechellia/)
FASTA
	dsec-all-CDS-r1.3.fasta.gz dsec-all-chromosome-r1.3.fasta.gz dsec-all-exon-r1.3.fasta.gz dsec-all-gene_extended2000-r1.3.fasta.gz dsec-all-gene-r1.3.fasta.gz dsec-all-intergenic-r1.3.fasta.gz dsec-all-intron-r1.3.fasta.gz dsec-all-predicted-r1.3.fasta.gz dsec-all-transcript-r1.3.fasta.gz dsec-all-translation-r1.3.fasta.gz
GFF
	dsec-all-r1.3.gff.gz dsec-gff_all_scaffolds-r1.3.tar.gz
Drosophila simulans (Dsim)
	Current Dsim FTP repository (ftp://flybase.net/genomes/Drosophila_simulans/current/) Current Dsim FTP FastA repository (ftp://flybase.net/genomes/Drosophila_simulans/current/fasta/) Current Dsim GFF repository (ftp://flybase.net/genomes/Drosophila_simulans/current/gff/) Dsim FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_simulans/)
FASTA
	dsim-all-CDS-r1.3.fasta.gz dsim-all-chromosome-r1.3.fasta.gz dsim-all-exon-r1.3.fasta.gz dsim-all-gene_extended2000-r1.3.fasta.gz dsim-all-gene-r1.3.fasta.gz dsim-all-intergenic-r1.3.fasta.gz dsim-all-intron-r1.3.fasta.gz dsim-all-predicted-r1.3.fasta.gz dsim-all-transcript-r1.3.fasta.gz dsim-all-translation-r1.3.fasta.gz
GFF
	dsim-all-r1.3.gff.gz dsim-gff_all_scaffolds-r1.3.tar.gz
Drosophila virilis (Dvir)
	Current Dvir FTP repository (ftp://flybase.net/genomes/Drosophila_virilis/current/) Current Dvir FTP FastA repository (ftp://flybase.net/genomes/Drosophila_virilis/current/fasta/) Current Dvir GFF repository (ftp://flybase.net/genomes/Drosophila_virilis/current/gff/) Dvir FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_virilis/)
FASTA
	dvir-all-CDS-r1.2.fasta.gz dvir-all-chromosome-r1.2.fasta.gz dvir-all-exon-r1.2.fasta.gz dvir-all-gene_extended2000-r1.2.fasta.gz dvir-all-gene-r1.2.fasta.gz dvir-all-intergenic-r1.2.fasta.gz dvir-all-intron-r1.2.fasta.gz dvir-all-predicted-r1.2.fasta.gz dvir-all-transcript-r1.2.fasta.gz dvir-all-translation-r1.2.fasta.gz
GFF
	dvir-all-r1.2.gff.gz dvir-gff_all_scaffolds-r1.2.tar.gz
Drosophila willistoni (Dwil)
	Current Dwil FTP repository (ftp://flybase.net/genomes/Drosophila_willistoni/current/) Current Dwil FTP FastA repository (ftp://flybase.net/genomes/Drosophila_willistoni/current/fasta/) Current Dwil GFF repository (ftp://flybase.net/genomes/Drosophila_willistoni/current/gff/) Dwil FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_willistoni/)
FASTA
	dwil-all-CDS-r1.3.fasta.gz dwil-all-chromosome-r1.3.fasta.gz dwil-all-exon-r1.3.fasta.gz dwil-all-gene_extended2000-r1.3.fasta.gz dwil-all-gene-r1.3.fasta.gz dwil-all-intergenic-r1.3.fasta.gz dwil-all-intron-r1.3.fasta.gz dwil-all-predicted-r1.3.fasta.gz dwil-all-transcript-r1.3.fasta.gz dwil-all-translation-r1.3.fasta.gz
GFF
	dwil-all-r1.3.gff.gz dwil-gff_all_scaffolds-r1.3.tar.gz
Drosophila yakuba (Dyak)
	Current Dyak FTP repository (ftp://flybase.net/genomes/Drosophila_yakuba/current/) Current Dyak FTP FastA repository (ftp://flybase.net/genomes/Drosophila_yakuba/current/fasta/) Current Dyak GFF repository (ftp://flybase.net/genomes/Drosophila_yakuba/current/gff/) Dyak FTP archive (ftp://ftp.flybase.net/genomes/Drosophila_yakuba/)
FASTA
	dyak-all-CDS-r1.3.fasta.gz dyak-all-chromosome-r1.3.fasta.gz dyak-all-exon-r1.3.fasta.gz dyak-all-gene_extended2000-r1.3.fasta.gz dyak-all-gene-r1.3.fasta.gz dyak-all-intergenic-r1.3.fasta.gz dyak-all-intron-r1.3.fasta.gz dyak-all-predicted-r1.3.fasta.gz dyak-all-transcript-r1.3.fasta.gz dyak-all-translation-r1.3.fasta.gz
GFF
	dyak-all-r1.3.gff.gz dyak-gff_all_scaffolds-r1.3.tar.gz
Transcripts and Polypeptides
Item Chado XML Reporting XML Other Transcript data download download Polypeptide data download download
Transposons, Transgenic Constructs, and Insertions
Item Chado XML Reporting XML Other Insertions download download Transgenic constructs download download Transgenic construct maps construct_maps.zip Map data for insertions insertion_mapping_fb_2013_03.tsv.gz Transposable elements (canonical set) transposon_sequence_set.embl.txt.gz
Aberrations
Item Chado XML Reporting XML Other Aberration data download download chromosome_images.zip Balancer data download download
Large Dataset Metadata
Item Chado XML Reporting XML Other Dataset metadata members dataset_metadata_fb_2013_03.tsv.gz
Clones
Item Chado XML Reporting XML Other Clone data download download cDNAs: FBcl ⇔ acc. ID cDNA_clone_data_fb_2013_03.tsv.gz Genomic: FBcl ⇔ acc. ID genomic_clone_data_fb_2013_03.tsv.gz
References
Item Chado XML Reporting XML Other Combined reference data download download FlyBase FBrf ⇔ PubMed ID fbrf_pmid_fb_2013_03.tsv.gz
Drosophila Researchers
	Addresses of Drosophila researchers are copyrighted (GSA) material and only provided for official business of the Fly Board.
Map Conversion Tables
Item Chado XML Reporting XML Other Cytological ⇔ Sequence genome-cyto-seq.txt.gz Cytological ⇔ Genetic cytotable.txt.gz Cyto ⇔ Genetic ⇔ Seq cyto-genetic-seq.tsv.gz Genes map table gene_map_table_fb_2013_03.tsv.gz