ArticleGenome research2003
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.Bioinformatics advances · 2025Review
- Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species.Communications biology · 2022Article
- Progress, Challenges, and Surprises in Annotating the Human Genome.Annual review of genomics and human genetics · 2020Review
- Whole-Genome Alignment and Comparative Annotation.Annual review of animal biosciences · 2019Review
- Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators.Nature genetics · 2017Article
- The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation.Genome biology · 2013Article
- Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.Genome research · 2012Article
- Genome majority vote improves gene predictions.PLoS computational biology · 2011Article
- Small open reading frames: current prediction techniques and future prospect.Current protein & peptide science · 2011Review
- Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition.Nature · 2010Article
- Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana.Plant cell reports · 2009Article
- Reranking candidate gene models with cross-species comparison for improved gene prediction.BMC bioinformatics · 2008Article
- Prediction of small, noncoding RNAs in bacteria using heterogeneous data.Journal of mathematical biology · 2008Article
- Targeted discovery of novel human exons by comparative genomics.Genome research · 2007Article
- Global discriminative learning for higher-accuracy computational gene prediction.PLoS computational biology · 2007Article
- Gene prediction: compare and CONTRAST.Genome biology · 2007Review
- Using ESTs to improve the accuracy of de novo gene prediction.BMC bioinformatics · 2006Article
- Comparative analysis of methylthioalkylmalate synthase (MAM) gene family and flanking DNA sequences in Brassica oleracea and Arabidopsis thaliana.Plant cell reports · 2006Article
- Iterative gene prediction and pseudogene removal improves genome annotation.Genome research · 2006Article
- Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.Genome biology · 2006Article
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Authors and funding
5 authors.
Funding
Abstract
The availability of draft sequences for both the mouse and human genomes makes it possible, for the first time, to annotate whole mammalian genomes using comparative methods. TWINSCAN is a gene-prediction system that combines the methods of single-genome predictors like GENSCAN with information derived from genome comparison, thereby improving accuracy. Because TWINSCAN uses genomic sequence only, it is less biased toward highly and/or ubiquitously expressed genes than GENEWISE, GENOMESCAN, and other methods based on evidence derived from transcripts. We show that TWINSCAN improves gene prediction in human using intermediate products from various stages of the sequencing and analysis of the mouse genome, from low-redundancy, whole-genome shotgun reads to the draft assembly and the synteny map. TWINSCAN improves on the prior state of the art even when alignments from only 1X coverage of the mouse genome are available. Gene prediction accuracy improves steadily from 1X through 3X, more slowly from 3X to 4X, and relatively little thereafter. The assembly and the synteny map greatly speed the computations, however. Our human annotation using the mouse assembly is conservative, predicting only 25,622 genes, and appears to be one of the best de novo annotations of the human genome to date.
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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.