Lmst

You can now search FlyBase and WormBase sequence data using the Alliance of Genome Resources BLAST server: www.alliancegenome.org/blastservice The Fly interface allows searching against many arthopods, or a search can be restricted to only Drosophila melanogaster databases.

#FlyBaseTootorial #AllianceGenomeTootorial #BLAST

Screenshot of the Alliance of Genome Resources BLAST page.
BLAST Service
Welcome to the BLAST Service for the Alliance of Genome Resources! This BLAST service allows researchers to search genomic sequences using the Basic Local Alignment Search Tool (BLAST). By entering a sequence or query, users can find regions of similarity to various genomes within the Alliance. This service supports separate environments for each of the Model Organism Databases (MODs) as well as a unified environment for the Alliance. Results provide detailed alignments and annotations to aid in your research. Explore the various BLAST environments through the links below to find the one that best suits your research needs:
Fly BLAST
Worm BLAST

Screenshot of the Alliance Fly BLAST, showing the options to search D. melanogaster nucleotide and protein databases.

New in FB2025_02: All Gene Group class pages,, including #SignalingPathway, #MetabolicPathway, #MacromolecularComplex and #GeneGroup reports, now have #InteractiveTables enabled.
As with other interactive tables, users can customize the 'Members' table by reordering or filtering columns, or filtering which columns to display.
#FlyBaseTootorial

Interactive table showing the genes comprising the SWR1 complex.

The Members table for the SWR1 complex. The 'Other Gene Groups' column has been dragged left so that it is now between the 'Also Known As' and 'Source Material for Membership' columns.

The Members table for the SWR1 complex. The text string 'Arp' has been entered in the "Also Known As" text box, so that the table is now limited to showing genes for which 'Arp*' is a synonym.

The Members table for the SWR1 complex with the 'Show/Hide Columns' menu opened. It's possible to choose to display or hide columns from a menu of menu of gene-associated data and reagents including Symbol, Name, Also Known As, number of Research References, Antibody, Disease Models (potential or experimental), Alleles, Transgenic constructs, Human Orthologs, Testis-Specificity Index, GO Molecular Function, EC Enzyme Name, Pathways, Cytogenetic map location. Source Material for Membership, and Other Gene Groups.

and a GO-Causal Activity Model (GO-CAM https://geneontology.org/docs/gocam-overview/) that is based directly on GO annotation data.

Useful links to external resources (FlyCyc, Reactome, KEGG) and publications are provided, as well as options to export the gene list to analysis, download and orthology tools.

For more information, see this Commentary: http://flybase.org/commentaries/2024_12/MetabolicPathways.html

#FlyBaseTootorial #GeneGroups #MetabolicPathways

A GO Causal Activity Model (GO-CAM) visual representation of the CHITIN SYNTHESIS metabolic pathway.

Links to external resources, including FlyCyc (chitin biosynthesis) and KEGG (Amino sugar and nucleotide sugar metabolism).

There's a surprise update to the #GAL4etc #QuickSearch tab!

As of today, the search results of this tab include #SplitSystemCombination hits.
#SplitGAL4 #hemidriver #FlyBaseTootorial

The FlyBase GAL4 etc QuickSearch tab. Only the 'Anatomy/Cell Type' field is filled, with the FlyBase Anatomy Controlled Vocabulary term 'alpha/beta surface Kenyon cell. The tab heading is boxed in purple.

As part of a collaboration with the EMBL-EBI Complex Portal https://www.ebi.ac.uk/complexportal/home many fly complexes have been added to this resource and 194 Macromolecular Complex Reports have corresponding entries.
#FlyBaseTootorial #MacromolecularComplexes #GeneGroups

The External Data section of the ACF COMPLEX FlyBase Macromolecular Complex group report. The link to the EMBL-EBI Complex Portal entry is boxed in pink.

The EMBL-EBI Complex Portal page for the Drosophila ACF chromatin remodeling complex.

Please check out this Commentary about the #GeneToolKit https://flybase.org/commentaries/2024_06/GeneToolkit.html
#FlyBaseTootorial

The combination pages have been added to hitlists, so if you search for a regulatory region that drives expression of one of the hemidrivers in a combination (e.g. R72B05, VT064569, ple) you'll see the relevant combination(s) in the hitlist.
These new report pages will get improvements during the coming months, including images of expression patterns when available.
#Split_GAL4
#hemidriver
#FlyBaseTootorial

Split-GAL4 combination reports as they appear in a FlyBase hitlist.

You can also find the Transgenic Product class on Allele and Transgenic Construct reports.

#FlyBaseTootorial #GeneticToolkit

FlyBase Recombinant Construct report, with the Transgenic product class boxed in purple.

FlyBase Allele report, with the Transgenic product class boxed in purple (two locations).

This release brings an update to #OrthoDB in FlyBase; we've worked with the OrthoDB https://www.orthodb.org/ team to implement a new API call that improves the accuracy of OrthoDB-derived #orthologs shown in FlyBase.
We use OrthoDB for ortholog calls of Dmel genes in many organisms (other than those represented in the FlyBase implementation of DIOPT), including other Drosophila species & arthropods.
@ensembl #FlyBaseTootorial

Click on the SO term in the “Transgenic product class” field of an Allele Report get a list of all transgenes encoding a particular type of gene product.
On the Term Report (located in the #Vocabularies tool http://flybase.org/vocabularies), you can click on the Alleles button to get a hit list of all of all the matching transgenic alleles.
#FlyBaseTootorial #TransgenicProductClass #SequenceOntology

Term Report for the Sequence Ontology term missense_variant. The Alleles box, which leads to a hit list of all transgenic alleles annotated with the term, is boxed in purple.

Did you know that FlyBase has a Papers with Technical Advances page in our External Resources? These papers have been suggested by authors as including a technical advance, new type of reagent, or resource likely to be useful for other researchers, and you can find it here: https://wiki.flybase.org/wiki/FlyBase:Papers_with_technical_advances. We update this resource every month with papers that authors have submitted by flagging during the Fast-Track Your Paper process. #FlyBaseTootorial #Technical_Advances

#FlyBaseTootorial

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