Difference between revisions of "FlyBase:Drosophila Online Resources"

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=Gene Expression Databases and Tools=
 
=Gene Expression Databases and Tools=
* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
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* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[https://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
 
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[https://www.bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
 
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[https://www.bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
 
* <b>DIGITtally</b>, Finding Genes of Interest DIGITtally: <br /> [https://www.digittally.org/ DIGITtally, University of Glasgow, Glasgow, UK]
 
* <b>DIGITtally</b>, Finding Genes of Interest DIGITtally: <br /> [https://www.digittally.org/ DIGITtally, University of Glasgow, Glasgow, UK]
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A summary table of selected GSEA tools with information about set up can be found [[FlyBase:GSEA|<b>here</b>]]
 
A summary table of selected GSEA tools with information about set up can be found [[FlyBase:GSEA|<b>here</b>]]
 
  
 
* <b>DAVID</b>, Database for Annotation, Visualization and Integrated Discovery :<br />[https://david.ncifcrf.gov/ DAVID, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA]]
 
* <b>DAVID</b>, Database for Annotation, Visualization and Integrated Discovery :<br />[https://david.ncifcrf.gov/ DAVID, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA]]
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* <b>Fly Labs and References</b>, a large list of fly labs and recent publications: <br />[https://www.sdbonline.org/sites/fly/flylabs/a.html Interactive Fly, Bethesda, MD, USA]
 
* <b>Fly Labs and References</b>, a large list of fly labs and recent publications: <br />[https://www.sdbonline.org/sites/fly/flylabs/a.html Interactive Fly, Bethesda, MD, USA]
 
* <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[https://academictree.org/flytree/ FlyTree, USA]
 
* <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[https://academictree.org/flytree/ FlyTree, USA]
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* <b>Fully automated drosophila wing landmarking</b>, Automatically finds more than 110 landmark points and creates a digital twin of the drosophila wing:<br />[https://datamarkin.com/models/drosophila-wings-beta/ Datamarkin, Marseille, France]
 
* <b>GenAge</b> -- The Ageing Gene Database:<br />[https://genomics.senescence.info/genes/index.html Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
 
* <b>GenAge</b> -- The Ageing Gene Database:<br />[https://genomics.senescence.info/genes/index.html Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
 
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[https://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[https://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
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* <b>MEROPS</b>, an information resource for peptidases:<br />[https://www.ebi.ac.uk/merops/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
 
* <b>MEROPS</b>, an information resource for peptidases:<br />[https://www.ebi.ac.uk/merops/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
 
* <b>ModBase</b>, Database of Comparative Protein Structure Models:<br />[https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase, UCSF, San Francisco, CA, USA]
 
* <b>ModBase</b>, Database of Comparative Protein Structure Models:<br />[https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase, UCSF, San Francisco, CA, USA]
* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
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* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[https://www.pantherdb.org/ Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 
* <b>PDB</b>, Protein Data Bank:<br />[https://www.rcsb.org/ PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* <b>PDB</b>, Protein Data Bank:<br />[https://www.rcsb.org/ PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://phosphopep.org/ Institute for Systems Biology, Seattle, Washington, USA]
 
* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://phosphopep.org/ Institute for Systems Biology, Seattle, Washington, USA]

Latest revision as of 13:33, 19 March 2024

Atlases, Images and Videos

Cell Lines and Cell Culture

CRISPRs and TALENs

Data Repositories

DNA Reagents

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Gene Set Enrichment Analysis

A summary table of selected GSEA tools with information about set up can be found here

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Metabolomics

Miscellaneous

Non-coding (ncRNA) Databases and Tools

General

lncRNA

miRNA

General

NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.
  • miRNEST, An integrated collection of miRNA predictions from high-throughput sequencing experiments and external database annotations (last updated 2015):
    miRNEST, The Adam Mickiewicz University in Poznan, Poznan, Poland
  • TransmiR, A database of transcription factor-microRNA regulation (last updated 2018):
    TransmiR, Peking University Health Science Center, Peking, Chin

miRNA Target Prediction

Validated miRNA Targets

Comparative miRNA Analysis

rRNA

tRNA

snoRNA

SRP RNA

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis and Modification

Public Education

RNAi

Sequence Analysis

Single Cell RNA-seq

  • VSN A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:
    VSN-Pipelines

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource