ArticleBMC bioinformatics2018
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 232 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
232 citing papers in PubMed.
- Archipelago architecture and evolution of paclitaxel biosynthesis revealed by the Pseudotaxus chienii haplotype-resolved genome.Nature communications · 2026Article
- Chromosome-scale Genome Assembly and Annotation of Anise Hyssop (Agastache foeniculum).Scientific data · 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
- Extreme conservation of cnidarian stinging cell identity despite 600 million years of evolution.bioRxiv : the preprint server for biology · 2026Article
- Chromosome-level genome assembly of the jumping spider Spartaeus platnicki.Scientific data · 2026Article
- A chromosomal-level genome assembly of Batocera lineolata Chevrolat, 1852 (Coleoptera: Cerambycidae).Scientific data · 2026Article
- A chromosomal-level genome assembly of Sinodiscula theae-sinensis strain Sthe1.Scientific data · 2026Article
- A structurally unique effector shared between vascular wilt fungi drives cotton and olive defoliation.Nature communications · 2026Article
- High-Quality Genome Assembly of the White King Pigeon for Genetic Reference of Chinese Market Pigeon Breeds.Scientific data · 2026Article
- Genomic contraction of theHorticulture research · 2026Article
- Cessation of Gene Flow Associated With the Reduction of a Sexually Selected Phenotype in the Island Stag Beetle.Molecular ecology · 2026Article
- Chromosome-level genome assembly of Manglietia pachyphylla.Scientific data · 2026Article
- Haplotype-resolved genome ofZoological research · 2026Article
- A chromosomal-level genome assembly of Nadezhdiella cantori (Hope, 1843) (Coleoptera: Cerambycidae).Scientific data · 2026Article
- Haplotype-resolved genome assembly of a cultivated variety of Zizania latifolia (Zhejiao7).Scientific data · 2026Article
- Chromosome-level genome assembly of Sinodiscula camellicola strain Scam5.Scientific data · 2026Article
- Chromosome-level genome assembly of Youngia japonica reveals evolutionary dynamics underlying adaptation in a synanthropic Asteraceae species.BMC plant biology · 2026Article
- The chromosome-level genome assembly of Sitobion avenae Fabricius (Hemiptera: Aphididae).Scientific data · 2026Article
- Comparative Genomics Provide Insights Into Karyotype Evolution in Vespertilionid Bats (Vespertilionidae, Chiroptera).Molecular ecology resources · 2026Article
- Haplotype-resolved genome sequences of a springtail species, Folsomia candida (Collembola: Isotomidae).Scientific data · 2026Article
172 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome annotation is of key importance in many research questions. The identification of protein-coding genes is often based on transcriptome sequencing data, ab-initio or homology-based prediction. Recently, it was demonstrated that intron position conservation improves homology-based gene prediction, and that experimental data improves ab-initio gene prediction.
resultsHere, we present an extension of the gene prediction program GeMoMa that utilizes amino acid sequence conservation, intron position conservation and optionally RNA-seq data for homology-based gene prediction. We show on published benchmark data for plants, animals and fungi that GeMoMa performs better than the gene prediction programs BRAKER1, MAKER2, and CodingQuarry, and purely RNA-seq-based pipelines for transcript identification. In addition, we demonstrate that using multiple reference organisms may help to further improve the performance of GeMoMa. Finally, we apply GeMoMa to four nematode species and to the recently published barley reference genome indicating that current annotations of protein-coding genes may be refined using GeMoMa predictions.
conclusionsGeMoMa might be of great utility for annotating newly sequenced genomes but also for finding homologs of a specific gene or gene family. GeMoMa has been published under GNU GPL3 and is freely available at http://www.jstacs.de/index.php/GeMoMa .
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.