ArticleSTAR protocols2021
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes.
Article in STAR protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- How has structuring your ideas into protocols contributed to your research progress and facilitated collaboration with others in the field?STAR protocols · 2025Article
- HSDSnake: a user-friendly SnakeMake pipeline for analysis of duplicate genes in eukaryotic genomes.Bioinformatics (Oxford, England) · 2025Article
- Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.G3 (Bethesda, Md.) · 2024Article
- PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation.Briefings in bioinformatics · 2024Article
- HSDatabase-a database of highly similar duplicate genes from plants, animals, and algae.Database : the journal of biological databases and curation · 2022Article
- TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.STAR protocols · 2022Article
- An overview of online resources for intra-species detection of gene duplications.Frontiers in genetics · 2022Review
- Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases.STAR protocols · 2021Article
- HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes.Frontiers in bioinformatics · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although gene duplications have been documented in many species, the precise numbers of highly similar duplicated genes (HSDs) in eukaryotic nuclear genomes remain largely unknown and can be time-consuming to explore. We developed HSDFinder to identify, categorize, and visualize HSDs in eukaryotic nuclear genomes using protein family domains and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In contrast to existing tools, HSDFinder allows users to compare HSDs among different species and visualize results in different KEGG pathway functional categories via heatmap plotting. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.