ArticleBMC genomics2008
WebScipio: an online tool for the determination of gene structures using protein sequences.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed.
- Genome-wide identification and characterization of active ingredients related β-Glucosidases in Dendrobium catenatum.BMC genomics · 2022Article
- Photoreceptor Diversification Accompanies the Evolution of Anthozoa.Molecular biology and evolution · 2021Article
- Exon-1 skipping and intron-1 retaining by alternative splicing of the c-KIT gene encodes a novel splice variant in the skin of Merino sheep (Ovis aries).Molecular biology reports · 2021Article
- Unicellular ancestry and mechanisms of diversification of Goodpasture antigen-binding protein.The Journal of biological chemistry · 2019 · on this mapArticle
- Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae.PloS one · 2018Article
- Article
- MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes.BMC evolutionary biology · 2014Article
- Molecular phylogeny of sequenced Saccharomycetes reveals polyphyly of the alternative yeast codon usage.Genome biology and evolution · 2014Article
- Predicting the fungal CUG codon translation with Bagheera.BMC genomics · 2014Article
- Shared gene structures and clusters of mutually exclusive spliced exons within the metazoan muscle myosin heavy chain genes.PloS one · 2014Article
- Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins.BMC evolutionary biology · 2013Article
- WebScipio: Reconstructing alternative splice variants of eukaryotic proteins.Nucleic acids research · 2013Article
- GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures.BMC bioinformatics · 2013Article
- Evolution of the eukaryotic dynactin complex, the activator of cytoplasmic dynein.BMC evolutionary biology · 2012Article
- Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.Mobile genetic elements · 2012Article
- Article
- A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function.BMC evolutionary biology · 2011Article
- Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio.BMC research notes · 2011Article
- Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology.BMC bioinformatics · 2011Article
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
backgroundObtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches.
resultsWebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs.
conclusionWebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org.
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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.