ArticleGenome biology2006
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed.
- From genomes to interventions: computational strategies transforming parasitology.Frontiers in veterinary science · 2026Review
- Genomes of Two Flying Squid Species Provide Novel Insights into Adaptations of Cephalopods to Pelagic Life.Genomics, proteomics & bioinformatics · 2022Article
- De novo screening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation.GigaScience · 2021Article
- Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive MycoparasiteJournal of fungi (Basel, Switzerland) · 2021Article
- A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Frontiers in genetics · 2021Article
- Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing.Biology · 2020Review
- Genomic Features ofPathogens (Basel, Switzerland) · 2020Article
- Article
- Toward point-of-care assessment of patient response: a portable tool for rapidly assessing cancer drug efficacy using multifrequency impedance cytometry and supervised machine learning.Microsystems & nanoengineering · 2019Article
- PalmXplore: oil palm gene database.Database : the journal of biological databases and curation · 2018Article
- Draft Genome Sequence and Annotation of the Apicomplexan ParasiteGenome announcements · 2017Article
- Evidence-based gene models for structural and functional annotations of the oil palm genome.Biology direct · 2017Article
- Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data.BMC bioinformatics · 2017Article
- Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.BMC genomics · 2015Article
- Improved transcript isoform discovery using ORF graphs.Bioinformatics (Oxford, England) · 2014Article
- MEGANTE: a web-based system for integrated plant genome annotation.Plant & cell physiology · 2014Article
- gff2sequence, a new user friendly tool for the generation of genomic sequences.BioData mining · 2013Article
- The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation.Genome biology · 2013Article
- Selecting one of several mating types through gene segment joining and deletion in Tetrahymena thermophila.PLoS biology · 2013Article
- Comparative genomic analysis and phylogenetic position of Theileria equi.BMC genomics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundPredicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet to emerge that can provide near perfect levels of sensitivity and specificity at the level of whole genes. As an incremental step in this direction, it is hoped that controlled gene finding experiments in the ENCODE regions will provide a more accurate view of the relative benefits of different strategies for modeling and predicting gene structures.
resultsHere we describe our general-purpose eukaryotic gene finding pipeline and its major components, as well as the methodological adaptations that we found necessary in accommodating human DNA in our pipeline, noting that a similar level of effort may be necessary by ourselves and others with similar pipelines whenever a new class of genomes is presented to the community for analysis. We also describe a number of controlled experiments involving the differential inclusion of various types of evidence and feature states into our models and the resulting impact these variations have had on predictive accuracy.
conclusionWhile in the case of the non-comparative gene finders we found that adding model states to represent specific biological features did little to enhance predictive accuracy, for our evidence-based 'combiner' program the incorporation of additional evidence tracks tended to produce significant gains in accuracy for most evidence types, suggesting that improved modeling efforts at the hidden Markov model level are of relatively little value. We relate these findings to our current plans for future research.
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.