ArticleNucleic acids research2009
Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genome annotation of disease-causing microorganisms.Briefings in bioinformatics · 2021Review
- A draft genome sequence of the elusive giant squid, Architeuthis dux.GigaScience · 2020Article
- Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus.Current genetics · 2019Article
- Draft Genome Sequence of an Obligate Psychrophilic Yeast,Genome announcements · 2017Article
- The genome of the hydatid tapeworm Echinococcus granulosus.Nature genetics · 2013Article
- TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.Frontiers in plant science · 2012Article
- New insight into praziquantel against various developmental stages of schistosomes.Parasitology research · 2011Review
- Approaches to Fungal Genome Annotation.Mycology · 2011Article
- Schistosomiasis in the People's Republic of China: the era of the Three Gorges Dam.Clinical microbiology reviews · 2010Review
- Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.BMC genomics · 2009Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a novel method for estimating the parameters of hidden Markov models for gene finding in newly sequenced species. Our approach does not rely on curated training data sets, but instead uses extrinsic evidence (including paired-end ditags that have not been used in gene finding previously) and iterative training. This new method is particularly suitable for annotation of species with large evolutionary distance to the closest annotated species. We have used our approach to produce an initial annotation of more than 16,000 genes in the newly sequenced Schistosoma japonicum draft genome. We established the high quality of our predictions by comparison to full-length cDNAs (withdrawn from the extrinsic evidence) and to CEGMA core genes. We also evaluated the effectiveness of the new training procedure on Caenorhabditis elegans genome. ExonHunter and the newest parametric files for S. japonicum genome are available for download at www.bioinformatics.uwaterloo.ca/downloads/exonhunter.
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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.