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Protocols

FlyBase specifications

Information


Unique identifier OMICS_01649
Name FlyBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 2.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/FlyBase

Taxon


  • Invertebrates
    • Drosophila melanogaster

Maintainer


  • person_outline Steven J. Marygold

Publications for FlyBase

library_books

Tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles

2014
PMCID: 3978375
PMID: 24715220
DOI: 10.1093/database/bau033

FlyBase citations

 (776)
library_books

Reduced Neuronal Transcription of Escargot, the Drosophila Gene Encoding a Snail Type Transcription Factor, Promotes Longevity

2018
Front Genet
PMCID: 5936762
PMID: 29760717
DOI: 10.3389/fgene.2018.00151

[…] le explanation of the crucial effect of the relatively small insertions on esg transcription rates is that they might perturb the integrity of hypothetical protein-binding platforms. According to the FlyBase analysis (FlyBase, 1992) of modENCODE data (The modENCODE Consortium et al., ) the insertion site co-localizes with a possible Transcription Factor Binding Motifs (TFBS) hotspot. At least one […]

library_books

De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

2018
Front Microbiol
PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] Drosophila melanogaster endoreplication mechanism involves the Delta-Notch signaling pathway, the main molecules involved in this process were obtained from KEGG and Flybase databases (Supplementary Table ).We searched the transcript coding for Aedes aegypti hindsight molecule in VectorBase database, Aedes aegypti Liverpool Strain, AaegL3 and AaegL3.4, genome and […]

library_books

Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT resistance in the Drosophila melanogaster strain 91 R

2018
PLoS One
PMCID: 5919617
PMID: 29698530
DOI: 10.1371/journal.pone.0196518

[…] he trimmed reads were quality-checked and curated using personal perl script. The results were aligned to the D. melanogaster reference genome (Release 6; dmel-all-chromosome-r6.19.fasta.gz at http://flybase.org/) using bowtie v.1.2.2 [] and also were mapped to D. melanogaster non-coding RNA database (dmel-all-tRNA-6.1/8.fasta and dmel-all-miscRNA-6.1/8.fasta file at flybase.org) in order to filte […]

library_books

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

2018
PLoS Genet
PMCID: 5933812
PMID: 29684059
DOI: 10.1371/journal.pgen.1007341

[…] apped all reads with bwa 0.7.15 using the BWA-MEM algorithm [] to the March 2012 release of the D. simulans assembly produced by Hu et al. [] and also used the accompanying annotation based on mapped FlyBase release 5.33 gene models []. Next, we removed duplicate fragments using Picard (https://github.com/broadinstitute/picard), before using GATK’s HaplotypeCaller (version 3.7; [–]) in discovery m […]

library_books

NCX DB: a unified resource for integrative analysis of the sodium calcium exchanger super family

2018
BMC Neurosci
PMCID: 5898058
PMID: 29649983
DOI: 10.1186/s12868-018-0423-2

[…] 2017) [] as well as the animal model organism databases that comprise the Alliance of Genome Resources (http://www.alliancegenome.org/). These are: WormBase (ver. WS260) [], XenBase (ver. 4.5.0) [], FlyBase (FB2017_04) [], the Zebrafish Information Network (ZFIN: https://zfin.org/), Mouse Genomics Informatics (http://www.informatics.jax.org/), and the Rat Genome Database (https://rgd.mcw.edu/). B […]

call_split

Identification of Candidate Iron Transporters From the ZIP/ZnT Gene Families in the Mosquito Aedes aegypti

2018
Front Physiol
PMCID: 5906682
PMID: 29706902
DOI: 10.3389/fphys.2018.00380
call_split See protocol

[…] Amino acid sequences for mosquito (Vectorbase.org), Drosophila (Flybase.org) or human (Genbank) ZIP (SLC39), ZnT (SLC30), and NRAMP (SLC11) genes were downloaded from the respective databases and aligned using ClustalW (Larkin et al., ) in MEGA6 (Tamura et al., ). […]

Citations

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FlyBase institution(s)
Department of Biology, Indiana University, Bloomington, IN, USA; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK; The Biological Laboratories, Harvard University, Cambridge, MA, USA
FlyBase funding source(s)
Supported by NIH, NHGRI [U41HG000739]; UK Medical Research Council [MR/N030117/1].

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