DAPHNIA BROWSER
Release history
Only user-facing feature additions and removals are recorded. Changes made on the same day are consolidated into one entry. Maintenance, fixes, coordinate adjustments, caching, wording, and visual refinements are not listed.
← Return to Daphnia BrowserVersion 1.6
Added
- Precomputed NIES supplementary annotation and cross-genome ID-to-NIES search with explicit RBH, ambiguous-hit, and isoform-consistency evidence.
- NIES Best-hit Annotation List for up to 500 supported Daphnia gene/protein/transcript IDs, with downloadable evidence tables and retained unmatched inputs.
Version 1.5
Added
- General browsing and analysis without an account. Sign in to unlock Lists & Batch Tools: ID conversion, gene lists, heatmaps, batch expression downloads, reports, and the Domain Browser.
Removed
- The Photo-lyase-only restriction for anonymous browsing.
Version 1.4
Added
- Added selectable target-proteome exploratory trees for all seven annotated Daphnia genomes using the 25 highest-bit-score gene-collapsed DIAMOND hits, visible identity and bilateral-coverage labels, evidence-tier colors, rectangular/circular views, and explicit weak-hit and non-orthology caveats.
Version 1.3
Added
- Added five genome annotations—Daphnia magna (Xinb3; APZ42 locus tags), Daphnia carinata (CSIRO-1), Daphnia sinensis (WSL), Daphnia pulicaria (SC F1-1A), and Daphnia pulex (KAP4)—with assembly-specific search, sequence export, Primer/CRISPR screening, exact ID conversion, and multi-species comparison.
- Added low-load all-genome gene search across all seven annotations, with genome-grouped candidates and explicit exact-ID, name/alias, and annotation-text match classes.
- Added cross-genome DIAMOND protein-similarity search with five ranked gene candidates, alignment metrics, reciprocal-best-hit evidence, and explicit partial-model and orthology caveats.
Removed
- Removed the cohort-wide LRV0_1 KO Variant Browser, including its embedded JBrowse view and filtered KO variant/candidate export workflow; the underlying research data and provenance remain archived outside the browser release.
Version 1.1
Added
- Guided Guest Demo using the Daphnia magna (NIES) Photo-lyase gene
LOC116919804, with access to the complete gene, sequence, expression, cached protein-evidence, primer/CRISPR, workbench, download, citation, and manual interfaces for that example. - Server-enforced scoping that blocks other genes, arbitrary sequences, unrestricted jobs, and protected project data while allowing the fixed demonstration workflow.
Version 1.0
Added
- Dual-assembly Daphnia magna (NIES) and Daphnia magna (LRV0_1) gene search, legacy ID conversion, annotation maps, and sequence/protein export.
- Published RNA-seq atlas, embryo expression evidence, multi-gene heatmaps, My Gene List, batch Excel, and printable gene reports.
- DIAMOND/Swiss-Prot annotation candidates, 22-species exploratory protein phylogeny, InterProScan Domain Atlas, and precomputed domain browsing.
- Primer design and conservative whole-genome specificity testing.
- Azimuth Rule Set 2 CRISPR activity scoring, official CFD per-site scoring, and bounded BLAST+ off-target candidate discovery.
- Methods and citations, provenance-aware downloads, English manual, and login-protected Jetstream2 private pilot.
Removed in Version 1.0
- Removed Body Length Measurement from Daphnia Browser.
- Removed the standalone Orthology Name Predictor and gene-name assignment workflow.
- Removed the approximate CRISPR activity and off-target scoring heuristics.
Versioning policy
Major versions indicate major redesigns or incompatible changes. Minor versions increase only when a meaningful user-facing feature is added or removed. Feature changes from the same date are combined into one entry; internal build numbers and maintenance work are not shown here.