Difference between revisions of "FlyBase:Drosophila Online Resources"

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* <b>Hieranoid</b>, An orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.<br />[https://hieranoid.sbc.su.se/index.html Hieranoid, Stockholm Bioinformatics Centre, Stockholm, Sweden]
 
* <b>Hieranoid</b>, An orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.<br />[https://hieranoid.sbc.su.se/index.html Hieranoid, Stockholm Bioinformatics Centre, Stockholm, Sweden]
 
* <b>HieranoiDB</b>, An online database of orthologs inferred by Hieranoid 2 for a representative set of proteomes.<br />[https://hieranoidb.sbc.su.se/ HieranoiDB, Stockholm Bioinformatics Centre, Stockholm, Sweden]
 
* <b>HieranoiDB</b>, An online database of orthologs inferred by Hieranoid 2 for a representative set of proteomes.<br />[https://hieranoidb.sbc.su.se/ HieranoiDB, Stockholm Bioinformatics Centre, Stockholm, Sweden]
* <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MD, USA]
+
* <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[https://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MD, USA]
 
* <b>InParanoiDB 9</b>, Ortholog groups with inparalogs for proteins and protein domains<br />[https://inparanoidb.sbc.su.se/about/ InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden]
 
* <b>InParanoiDB 9</b>, Ortholog groups with inparalogs for proteins and protein domains<br />[https://inparanoidb.sbc.su.se/about/ InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden]
 
* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://groups.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]
 
* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://groups.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]

Revision as of 21:39, 20 February 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