FlyBase

Database on Drosophilidae genetics

FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae.[1] For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different formats.

Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. These data types include mutant phenotypes; molecular characterization of mutant alleles; and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models, and molecular classification of gene product functions.[2] Query tools allow navigation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. The database offers several different query tools in order to provide efficient access to the data available and facilitate the discovery of significant relationships within the database.[3] Links between FlyBase and external databases, such as BDGP[4] or modENCODE,[5] provide opportunities for further exploration into other model organism databases and other resources of biological and molecular information.[6] The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at Harvard University and Indiana University in the United States, and University of Cambridge in the United Kingdom.

FlyBase is one of the organizations contributing to the Generic Model Organism Database (GMOD).[7]

As of 2022[update] the FlyBase home page requested a website access fee of US$150.00 per person per year, stating that "The NHGRI has reduced the funding of FlyBase by 50%".[8]

## Background

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Drosophila melanogaster has been an experimental organism since the early 1900s, and has since been placed at the forefront of many areas of research.[9] As this field of research spread and became global, researchers working on the same problems needed a way to communicate and monitor progress in the field. This niche was initially filled by community newsletters such as the Drosophila Information Service (DIS), which dates back to 1934 when the field was starting to spread from Thomas Hunt Morgan's lab. Material in these pages presented regular 'catalogs' of mutations, and bibliographies of the Drosophila literature. As computer infrastructure developed in the '80s and '90s, these newsletters gave way and merged with internet mailing lists, and these eventually became online resources and data. In 1992, data on the genetics and genomics of D. melanogaster and related species were electronically available over the Internet through the funded FlyBase, BDGP (Berkeley Drosophila Genome Project) and EDGP (European Drosophila Genome Project) informatics groups. These groups recognized that most genome project and community data types overlapped. They decided it would be of value to present the scientific community with an integrated view of the data. In October 1992, the National Center for Human Genome Research of the NIH funded the FlyBase project with the objective of designing, building and releasing a database of genetic and molecular information concerning Drosophila melanogaster. FlyBase also receives support from the Medical Research Council, London.[10] In 1998, the FlyBase consortium integrated the information into a single Drosophila genomics server. As of 2022[update] the FlyBase project was carried out by a consortium of Drosophila researchers and computer scientists at Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.[11]

## Contents

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FlyBase contains a complete annotation of the Drosophila melanogaster genome that is updated several times per year.[12] It also included a searchable bibliography of research on Drosophila genetics in the last century. Information on current researchers, and a partial pedigree of relationships between current researchers, was searchable, based on registration of the participating scientist.[13] The site also provides a large database of images illustrating the full genome, and several movies detailing embryogenesis (ImageBrowser Archived 2007-03-24 at the Wayback Machine). The two major tributaries to the database are the large multispecies data sets deposited by the Drosophila 12 Genomes Consortium (Clark et al 2007) and Crosby et al 2007.[14]

Search Strategies—Gene reports for genes from all twelve sequenced Drosophila genomes are available in FlyBase. There are four main ways this data can be browsed: Precomputed Files[15] BLAST,[16] Gbrowse,[17] and Gene Report Pages. Gbrowse and precomputed files are for genome-wide analysis, bioinformatics, and comparative genomics. BLAST and gene report pages are for a specific gene, protein, or region across the species.

When looking for cytology there are two main tools available. Use Cytosearch[18] when looking for cytologically-mapped genes or deficiencies, that have not been molecularly mapped to the sequence. Use Gbrowse when looking for molecularly mapped sequences, insertions, or Affymetrix probes.

There are two main query tools in FlyBase. The first main query tool is called Jump to Gene (J2G). This is found in the top right of the blue navigation bar on every page of FlyBase. This tool is useful when you know exactly what you are looking for and want to go to the report page with that data. The second main query tool is called QuickSearch. This is located on the FlyBase homepage. This tool is most useful when you want to look up something quickly that you may only know a little about. Searching can be performed within D. melanogaster only or within all species. Data other than genes can be searched using the ‘data class’ menu.

## Related research

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The following provides two examples of research that is related to or uses FlyBase:

* The first is a study of expressed genes from alate (meaning "having wings") Toxoptera citricida, more commonly known as the brown citrus aphid. The brown citrus aphid, is considered the primary vector of citrus tristeza virus, a severe pathogen which causes losses to citrus industries worldwide. The winged form of this aphid can fly long distances with the wind, enabling them to spread the citrus tristeza virus in citrus growing regions. To better understand the biology of the brown citrus aphid and the emergence of genes expressed during wing development, researchers undertook a large-scale 5′ end sequencing project of cDNA clones from winged aphids. Similar large-scale expressed sequence tag (EST) sequencing projects from other insects have provided a vehicle for answering biological questions relating to development and physiology. Although there is a growing database in GenBank of ESTs from insects, most are from Drosophila melanogaster, with relatively few specifically derived from aphids. The researchers were able to provide a large data set of ESTs from the alate (winged) brown citrus aphid and have begun to analyze this valuable resource. They were able to do this with the help of information on Drosophila melanogaster in FlyBase. Putative sequence identity was determined using BLAST searches. Sequence matches with E-value scores ≤ −10 were considered significant and were categorized according to the Gene Ontology (GO) classification system based on annotation of the 5 ‘best hit’ matches in BLASTX searches. All D. melanogaster matches were cataloged using FlyBase. Nearly all of these ‘best hit’ matches were characterized with respect to the functionally annotated genes in D. melanogaster using FlyBase. Genetic information is crucial to advancing the understanding of aphid biology, and will play a major role in the development of future non-chemical, gene-based control strategies against these insect pests.[19]
* Enhancing Drosophila Gene Ontology Annotation: What gene products do and where they do it are important questions for biologists. The Gene Ontology project was established 13 years ago in order to summarize this data consistently across different databases by using a common set of defined vocabulary terms. They also encode relationships between terms. The Gene Ontology Project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project also provides gene product annotation data from GO consortium members.[20] FlyBase was one of the three founding members of the Gene Ontology Consortium. GO annotation comprises at least three components: a GO term that describes molecular function, biological role, or subcellular location; an "evidence code" that describes the type of analysis used to support the GO term; and an attribution to a specific reference. GO annotation is useful for both small-scale and large-scale analyses. It can provide a first indication of the nature of a gene product and, in conjunction with evidence codes, point directly to papers with pertinent experimental data. The current priorities for annotation are: homologs of human disease genes, genes that are highly conserved across species, genes involved in biochemical/signaling pathways, and topical genes shown to be of significant interest in recent publications. FlyBase has been contributing GO annotations to the project since it started in August 2006. GO annotations appear on the Gene Report page in FlyBase. GO data are searchable in FlyBase using both TermLink and QueryBuilder. The GO is dynamic and can change on a daily basis, for example the addition of new terms. To keep up, FlyBase loads a new version of the GO every one or two releases of FlyBase. The GO annotation set is submitted to the GOC at the same time as a new version of FlyBase is released.[21]

## See also

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* List of Drosophila databases
* Model Organism Databases
* WormBase
* Xenbase

## Notes and references

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1. ^ Thurmond, Jim; Goodman, Joshua L; Strelets, Victor B; Attrill, Helen; Gramates, L Sian; Marygold, Steven J; Matthews, Beverley B; Millburn, Gillian; Antonazzo, Giulia; Trovisco, Vitor; Kaufman, Thomas C; Calvi, Brian R; Perrimon, Norbert; Gelbart, Susan Russo; Agapite, Julie; Broll, Kris; Crosby, Lynn; Santos, Gilberto dos; Emmert, David; Gramates, L Sian; Falls, Kathleen; Jenkins, Victoria; Matthews, Beverley; Sutherland, Carol; Tabone, Christopher; Zhou, Pinglei; Zytkovicz, Mark; Brown, Nick; Antonazzo, Giulia; Attrill, Helen; Garapati, Phani; Holmes, Alex; Larkin, Aoife; Marygold, Steven; Millburn, Gillian; Pilgrim, Clare; Trovisco, Vitor; Urbano, Pepe; Kaufman, Thomas; Calvi, Brian; Czoch, Bryon; Goodman, Josh; Strelets, Victor; Thurmond, Jim; Cripps, Richard; Baker, Phillip (8 January 2019). "FlyBase 2.0: the next generation". Nucleic Acids Research. 47 (D1): D759 – D765. doi:10.1093/nar/gky1003. PMC 6323960. PMID 30364959.
2. ^ Crosby, Madeline A; et al. (2007). "FlyBase: Genomes by the Dozen". Nucleic Acids Research. 35 (Database issue). Oxford Journals: D486 – D491. doi:10.1093/nar/gkl827. PMC 1669768. PMID 17099233.
3. ^ Wilson, RJ; Goodman, JL; Strelets, VB (2008). "FlyBase: integration and improvements to query tools". Nucleic Acids Res. 36 (Database issue): D588–93. doi:10.1093/nar/gkm930. PMC 2238994. PMID 18160408.
4. ^ BDGP
5. ^ modENCODE
6. ^ Drysdale, R (2008). "FlyBase: A Database for the Drosophila Research Community". Drosophila. Methods Mol. Biol. Vol. 420\. pp. 45–59\. doi:10.1007/978-1-59745-583-1_3. ISBN 978-1-58829-817-1. PMID 18641940.
7. ^ Generic Model Organism Database (GMOD).
8. ^ "Home page". FlyBase. Retrieved 24 April 2022.
9. ^ Pete Geiger (2002). "An Introduction to Drosophila Melanogaster". BIOLOGY.ARIZONA.EDU. Archived from the original on 2 August 2013.
10. ^ Gelbart, WM; Crosby, M; Matthews, B; Rindone, WP; Chillemi, J; Russo Twombly, S; Emmert, D; Ashburner, M; Drysdale, RA; Whitfield, E; Millburn, GH; de Grey, A; Kaufman, T; Matthews, K; Gilbert, D; Strelets, V; Tolstoshev, C (1997). "FlyBase: a Drosophila database. The FlyBase consortium". Nucleic Acids Res. 25 (1): 63–6\. doi:10.1093/nar/25.1.63. PMC 146418. PMID 9045212.
11. ^ "FlyBase:About - FlyBase Consortium". Flybase wiki. Retrieved 24 April 2022.
12. ^ Drysdale, Rachel; Flybase Consortium (2008-07-19). "FlyBase: A Database for the Drosophila Research Community". In Dahmann, Christian (ed.). Drosophila. Methods in Molecular Biology. Vol. 420\. Totowa, New Jersey, USA: Humana Press. pp. 45–59\. doi:10.1007/978-1-59745-583-1_3. ISBN 978-1-58829-817-1. PMID 18641940.
13. ^ "Find a Person". Archived from the original on 25 May 2019.
14. ^ Tweedie, Susan; Ashburner, Michael; Falls, Kathleen; Leyland, Paul; McQuilton, Peter; Marygold, Steven; Millburn, Gillian; Osumi-Sutherland, David; Schroeder, Andrew; Seal, Ruth; Zhang, Haiyan; The FlyBase Consortium (2009-01-01). "FlyBase: enhancing Drosophila Gene Ontology annotations". Nucleic Acids Research. 37 (Database). OUP: D555 – D559. doi:10.1093/nar/gkn788. ISSN 0305-1048. PMC 2686450. PMID 18948289. S2CID 332782.
15. ^ Precomputed Files
16. ^ BLAST
17. ^ Gbrowse
18. ^ "Cytosearch". Archived from the original on 2011-10-07. Retrieved 2011-11-24.
19. ^ Hunter, WB; Dang, PM; Bausher, MG; Chaparro, JX; McKendree, W; Shatters, RG; McKenzie, CL; Sinisterra, XH (2003). "Aphid biology: expressed genes from alate Toxoptera citricida, the brown citrus aphid". J. Insect Sci. 3: 23. doi:10.1093/jis/3.1.23. PMC 524662. PMID 15841239.
20. ^ "The Gene Ontology". Retrieved 31 May 2017.
21. ^ Tweedie, Susan; et al. (2009). "FlyBase: Enhancing Drosophila Gene Ontology Annotations". Nucleic Acids Research. 37 (Database issue). Oxford Journals: D555 – D559. doi:10.1093/nar/gkn788. PMC 2686450. PMID 18948289.

## External links

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* Official Site

* v
* t
* e

Bioinformatics

Databases|

* Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
* Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
* Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
* Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network

Software|

* BLAST
* Bowtie
* Clustal
* EMBOSS
* HMMER
* MUSCLE
* PANGOLIN
* SAMtools
* SOAP suite
* TopHat

Other|

* Server: ExPASy
* Rosalind (education platform)

Institutions|

* Broad Institute
* Computational Biology Department (CBD)
* Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
* Database Center for Life Science (DBCLS)
* DNA Data Bank of Japan (DDBJ)
* European Bioinformatics Institute (EMBL-EBI)
* European Molecular Biology Laboratory (EMBL)
* Flatiron Institute
* J. Craig Venter Institute (JCVI)
* Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
* US National Center for Biotechnology Information (NCBI)
* Japanese Institute of Genetics
* Netherlands Bioinformatics Centre (NBIC)
* Philippine Genome Center (PGC)
* Scripps Research
* Swiss Institute of Bioinformatics (SIB)
* Wellcome Sanger Institute
* Whitehead Institute

Organizations|

* African Society for Bioinformatics and Computational Biology (ASBCB)
* Australia Bioinformatics Resource (EMBL-AR)
* European Molecular Biology network (EMBnet)
* International Nucleotide Sequence Database Collaboration (INSDC)
* International Society for Biocuration (ISB)
* International Society for Computational Biology (ISCB)
* Student Council (ISCB-SC)
* Institute of Genomics and Integrative Biology (CSIR-IGIB)
* Japanese Society for Bioinformatics (JSBi)

Meetings|

* Basel Computational Biology Conference‎ ([BC2])
* European Conference on Computational Biology (ECCB)
* Intelligent Systems for Molecular Biology (ISMB)
* International Conference on Bioinformatics (InCoB)
* International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
* ISCB Africa ASBCB Conference on Bioinformatics
* Pacific Symposium on Biocomputing (PSB)
* Research in Computational Molecular Biology (RECOMB)

File formats|

* CRAM format
* FASTA format
* FASTQ format
* NeXML format
* Nexus format
* Pileup format
* SAM format
* Stockholm format
* VCF format
* GFF format
* GTF format

Related topics|

* Computational biology
* List of biobanks
* List of biological databases
* Molecular phylogenetics
* Sequencing
* Sequence database
* Sequence alignment

* Category
* Commons

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