ArticleNucleic acids research2016
Using intron position conservation for homology-based gene prediction.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 486 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
486 citing papers in PubMed.
- Article
- Infection mechanisms ofiMeta · 2026Article
- Genomic insights into trichome and inflorescence evolution of the palaeopolyploid tree genus Greyia.The Plant journal : for cell and molecular biology · 2026Article
- Divergent genome fractionation and adaptation following polyploidy in the Araliaceae.Nature communications · 2026Article
- Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.Molecular biology and evolution · 2026Article
- Chromosome-level Streptochaeta genome elucidates the ancestral karyotype and allopolyploid origin of grasses.Nature communications · 2026Article
- Isolation, Biocontrol Efficacy and Genomic Analysis ofMicroorganisms · 2026Article
- Chromosome-scale genome assembly of Artabotrys hexapetalus provides insights into its evolution and terpenoid biosynthesis.BMC plant biology · 2026Article
- Mating-Type System Analysis and Domestication ofJournal of fungi (Basel, Switzerland) · 2026Article
- Convergent Functional Genomic Evolution Underlying Repeated Freshwater Colonization in Cetaceans.Journal of molecular evolution · 2026Article
- Identification and Characterization of Genes Associated With Wood Property Traits via Genome Sequencing in Fast-Growing Species of GenusEvolutionary applications · 2026Article
- Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms.Cell reports · 2026Article
- Dissecting flowering time and flower color in Carum carvi utilizing a long-read draft genome and a GBS-based QTL mapping.Scientific reports · 2026Article
- Chromosome-scale genome assembly and annotation of Jonah's icefish Neopagetopsis ionah.Scientific data · 2026Article
- Extreme conservation of cnidarian stinging cell identity despite 600 million years of evolution.bioRxiv : the preprint server for biology · 2026Article
- The Trichinella Super-Pangenome Reveals the Evolution of Encapsulation and Predicted Host-Parasite Protein Interactions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Chromosome-level genome assembly and population genomics unveil strigolactone-regulated growth adaptation in the mycoheterotrophic orchidHorticulture research · 2026Article
- A structurally unique effector shared between vascular wilt fungi drives cotton and olive defoliation.Nature communications · 2026Article
- A domestication gene links plant architecture and nitrogen metabolism to enhance yield in foxtail millet.Nature communications · 2026Article
- High-Quality Genome Assembly of the White King Pigeon for Genetic Reference of Chinese Market Pigeon Breeds.Scientific data · 2026Article
426 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Annotation of protein-coding genes is very important in bioinformatics and biology and has a decisive influence on many downstream analyses. Homology-based gene prediction programs allow for transferring knowledge about protein-coding genes from an annotated organism to an organism of interest.Here, we present a homology-based gene prediction program called GeMoMa. GeMoMa utilizes the conservation of intron positions within genes to predict related genes in other organisms. We assess the performance of GeMoMa and compare it with state-of-the-art competitors on plant and animal genomes using an extended best reciprocal hit approach. We find that GeMoMa often makes more precise predictions than its competitors yielding a substantially increased number of correct transcripts. Subsequently, we exemplarily validate GeMoMa predictions using Sanger sequencing. Finally, we use RNA-seq data to compare the predictions of homology-based gene prediction programs, and find again that GeMoMa performs well.Hence, we conclude that exploiting intron position conservation improves homology-based gene prediction, and we make GeMoMa freely available as command-line tool and Galaxy integration.
Indexed as
Identifiers
What OpenQuestion holds
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.