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Journal Article
Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species
Database, Volume 2026, 2026, baag035, https://doi.org/10.1093/database/baag035
Published: 29 June 2026
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Architecture and workflow of the CypriSSR database. Genome assemblies and g...
Published: 29 June 2026
Figure 2
Architecture and workflow of the CypriSSR database. Genome assemblies and gene annotation files obtained from NCBI are processed through a computational pipeline for SSR identification, functional classification, and primer design. The resulting data are stored in a MySQL-based backend and accesse
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Distribution of microsatellite repeat types across eleven cyprinid species....
Published: 29 June 2026
Figure 3
Distribution of microsatellite repeat types across eleven cyprinid species. The y-axis represents the percentage distribution of microsatellite repeat types, while the x-axis lists the species. Three-dimensional bar chart showing the percentage distribution of microsatellite (SSR) repeat types ac
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Workflow for genome-wide microsatellite (SSR) identification and developmen...
Published: 29 June 2026
Figure 1
Workflow for genome-wide microsatellite (SSR) identification and development of the CypriSSR database. Workflow illustrating the development of the CypriSSR database. Genome assemblies were collected from NCBI GenBank/RefSeq and preprocessed into chromosome-wise genome files. SSRs were identifi
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Distribution of genic and non-genic SSRs across six cyprinid species. The y...
Published: 29 June 2026
Figure 4
Distribution of genic and non-genic SSRs across six cyprinid species. The y-axis represents the total number of identified SSRs, while the x-axis shows the species. Line graph showing the distribution of genic and non-genic SSRs across six cyprinid species: Cyprinus carpio, Labeo rohita, Carassiu
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Overview of the CypriSSR database workflow and user interface.(A) Homepage ...
Published: 29 June 2026
Figure 5
Overview of the CypriSSR database workflow and user interface.(A) Homepage providing access to database tools and general information. (B) Species selection panel displaying available fish species.(C) Statistics page showing SSR distribution and summary statistics.(D) Tool section for sequence inp
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Key functionalities and applications of the CypriSSR database. This graphic...
Published: 29 June 2026
Figure 6
Key functionalities and applications of the CypriSSR database. This graphical summary highlights major features, including genetic diversity assessment, aquaculture breeding, conservation genomics, comparative genomics, a user-friendly BLAST tool, and database visualization and export capabilities
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Overview of the strategy employed to develop and expand KitBase, the Kitaak...
Published: 12 June 2026
Figure 1
Overview of the strategy employed to develop and expand KitBase, the KitaakeX rice FN mutagenized population. (A) M 0 generation KitaakeX seeds were subjected to FN irradiation, and the resulting M 1 plants were self-fertilized to produce M 2 seeds. (B) Seeds from 3268 M 2 or M 3 mutant lines w
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Genome-Wide Characterization of Mutations in 3268 FN-Induced Rice Mutant Li...
Published: 12 June 2026
Figure 2
Genome-Wide Characterization of Mutations in 3268 FN-Induced Rice Mutant Lines. (A) The number of mutant lines aligned to each reference genome (Nipponbare and KitaakeX), showing the distribution of sequencing data for comparative genomic analysis. (B) Distribution of mutant lines based on the numbe
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Representative phenotypes observed in FN-mutagenized KitaakeX rice lines. T...
Published: 12 June 2026
Figure 6
Representative phenotypes observed in FN-mutagenized KitaakeX rice lines. This figure displays a range of morphological alterations induced by FN mutagenesis in the KitaakeX population. (A) Panicle height: tall to dwarf; (B) Lethal albino seedling; (C) Leaf phenotypes: partial albino, brown and mimi
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Overview of the KitBase User Interface. (A) Main Navigation Page: Displays ...
Published: 12 June 2026
Figure 7
Overview of the KitBase User Interface. (A) Main Navigation Page: Displays the primary navigation menu at the top and bottom, facilitating access to various sections of KitBase. (B) Search Functionality: Offers multiple search options, including Mutant ID, Gene ID, Keyword, and Phenotype, enabling u
Journal Article
KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants
Database, Volume 2026, 2026, baag024, https://doi.org/10.1093/database/baag024
Published: 12 June 2026
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Comprehensive Analysis of Affected Genes in 3268 FN-Induced Rice Mutant Lin...
Published: 12 June 2026
Figure 3
Comprehensive Analysis of Affected Genes in 3268 FN-Induced Rice Mutant Lines. (A) Left: Proportion of annotated genes affected by FN-induced mutations in the Nipponbare and KitaakeX reference genomes, without subdivision of transposable element (TE) and non-TE gene categories. Right: Proportion of
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Chromosomal Distribution and Mutation Density of Affected Genes. (A) Chromo...
Published: 12 June 2026
Figure 4
Chromosomal Distribution and Mutation Density of Affected Genes. (A) Chromosomal mapping of affected genes in the Nipponbare alignment. The heatmap represents the number of distinct mutations per gene, ranging from lighter shades (yellow, indicating one mutation) to darker shades (red, indicating te
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Chromosomal Distribution and Frequency of Mutation Types in the FN-Induced ...
Published: 12 June 2026
Figure 5
Chromosomal Distribution and Frequency of Mutation Types in the FN-Induced Kitaake Rice Mutant Population. (A) Circular plot showing the distribution and frequency of mutations across the 12 rice chromosomes on a megabase scale. The plot consists of six concentric tracks, labeled A–F from outermost
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Lysins identified in the EnVhog database. (A) The number of proteins, stand...
Published: 05 June 2026
Figure 4
Lysins identified in the EnVhog database. (A) The number of proteins, standard clusters (30% sequence identity), and remote homology clusters predicted by SUBLYME, split according to lysin type (endolysin and virion associated lysin—VAL). (B) Number of representative endolysins (one per standard clu
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Domain architecture occurrences in PhaLP 2.0. More specific annotations are...
Published: 05 June 2026
Figure 5
Domain architecture occurrences in PhaLP 2.0. More specific annotations are listed below the principal architecture; only the most frequent ones are listed. Enzymatically active domains (EADs) are presented in red, cell wall-binding domains (CBDs) in blue, and miscellaneous domains in yellow. Sch
Journal Article
A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs
Database, Volume 2026, 2026, baag022, https://doi.org/10.1093/database/baag022
Published: 05 June 2026
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Hierarchical clustering of publication types by model-inferred probabilitie...
Published: 05 June 2026
Figure 3
Hierarchical clustering of publication types by model-inferred probabilities. Publication type clusters derived from pairwise model score correlations and grouped with hierarchical clustering. Cut points were chosen to delineate 13 low-level categories and 5 broader categories. Diagram showing th
Journal Article
PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery
Database, Volume 2026, 2026, baag033, https://doi.org/10.1093/database/baag033
Published: 05 June 2026
