Improved annotation with de novo transcriptome assembly in four social amoeba species. Singh, R., Lawal, H. M., Schilde, C., Glöckner, G., Barton, G. J., Schaap, P., & Cole, C. BMC Genomics, 18:120, January, 2017. ![Improved annotation with de novo transcriptome assembly in four social amoeba species [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.
@article{singh_improved_2017,
title = {Improved annotation with de novo transcriptome assembly in four social amoeba species},
volume = {18},
issn = {1471-2164},
url = {http://dx.doi.org/10.1186/s12864-017-3505-0},
doi = {10.1186/s12864-017-3505-0},
abstract = {Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.},
urldate = {2017-01-31},
journal = {BMC Genomics},
author = {Singh, Reema and Lawal, Hajara M. and Schilde, Christina and Glöckner, Gernot and Barton, Geoffrey J. and Schaap, Pauline and Cole, Christian},
month = jan,
year = {2017},
keywords = {DAG, De novo, Dictyostelia, RNA-seq, Social amoeba, Transcriptome assembly, mine},
pages = {120}
}
Downloads: 0
{"_id":"7xPtHJHj5jCYvQLMg","bibbaseid":"singh-lawal-schilde-glckner-barton-schaap-cole-improvedannotationwithdenovotranscriptomeassemblyinfoursocialamoebaspecies-2017","downloads":0,"creationDate":"2017-02-01T11:44:44.580Z","title":"Improved annotation with de novo transcriptome assembly in four social amoeba species","author_short":["Singh, R.","Lawal, H. M.","Schilde, C.","Glöckner, G.","Barton, G. J.","Schaap, P.","Cole, C."],"year":2017,"bibtype":"article","biburl":"https://api.zotero.org/users/4242294/collections/XX294CEM/items?key=EeXceUMrWqGRvEcfKLsXMsp7&format=bibtex&limit=100","bibdata":{"bibtype":"article","type":"article","title":"Improved annotation with de novo transcriptome assembly in four social amoeba species","volume":"18","issn":"1471-2164","url":"http://dx.doi.org/10.1186/s12864-017-3505-0","doi":"10.1186/s12864-017-3505-0","abstract":"Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.","urldate":"2017-01-31","journal":"BMC Genomics","author":[{"propositions":[],"lastnames":["Singh"],"firstnames":["Reema"],"suffixes":[]},{"propositions":[],"lastnames":["Lawal"],"firstnames":["Hajara","M."],"suffixes":[]},{"propositions":[],"lastnames":["Schilde"],"firstnames":["Christina"],"suffixes":[]},{"propositions":[],"lastnames":["Glöckner"],"firstnames":["Gernot"],"suffixes":[]},{"propositions":[],"lastnames":["Barton"],"firstnames":["Geoffrey","J."],"suffixes":[]},{"propositions":[],"lastnames":["Schaap"],"firstnames":["Pauline"],"suffixes":[]},{"propositions":[],"lastnames":["Cole"],"firstnames":["Christian"],"suffixes":[]}],"month":"January","year":"2017","keywords":"DAG, De novo, Dictyostelia, RNA-seq, Social amoeba, Transcriptome assembly, mine","pages":"120","bibtex":"@article{singh_improved_2017,\n\ttitle = {Improved annotation with de novo transcriptome assembly in four social amoeba species},\n\tvolume = {18},\n\tissn = {1471-2164},\n\turl = {http://dx.doi.org/10.1186/s12864-017-3505-0},\n\tdoi = {10.1186/s12864-017-3505-0},\n\tabstract = {Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.},\n\turldate = {2017-01-31},\n\tjournal = {BMC Genomics},\n\tauthor = {Singh, Reema and Lawal, Hajara M. and Schilde, Christina and Glöckner, Gernot and Barton, Geoffrey J. and Schaap, Pauline and Cole, Christian},\n\tmonth = jan,\n\tyear = {2017},\n\tkeywords = {DAG, De novo, Dictyostelia, RNA-seq, Social amoeba, Transcriptome assembly, mine},\n\tpages = {120}\n}\n\n","author_short":["Singh, R.","Lawal, H. M.","Schilde, C.","Glöckner, G.","Barton, G. J.","Schaap, P.","Cole, C."],"key":"singh_improved_2017","id":"singh_improved_2017","bibbaseid":"singh-lawal-schilde-glckner-barton-schaap-cole-improvedannotationwithdenovotranscriptomeassemblyinfoursocialamoebaspecies-2017","role":"author","urls":{"Paper":"http://dx.doi.org/10.1186/s12864-017-3505-0"},"keyword":["DAG","De novo","Dictyostelia","RNA-seq","Social amoeba","Transcriptome assembly","mine"],"downloads":0},"search_terms":["improved","annotation","novo","transcriptome","assembly","four","social","amoeba","species","singh","lawal","schilde","glöckner","barton","schaap","cole"],"keywords":["dag","de novo","dictyostelia","rna-seq","social amoeba","transcriptome assembly","mine"],"authorIDs":[],"dataSources":["BoGsm9ca8tJL67c5b"]}