WormBase 2017: molting into a new stage

Lee, Raymond Y. N.; Howe, Kevin; Harris, Todd W.; Arnaboldi, Valerio; Cain, Scott; Chan, Juancarlos; Chen, Wen J.; Davis, Paul A.; Gao, Sibyl; Grove, Christian A.; Kishore, Ranjana; Müller, Hans‐Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael; Raciti, Daniela; Rodgers, Faye H.; Russell, Matthew; Schindelman, Gary; Tuli, Mary Ann; Auken, Kimberly Van; Wang, Qinghua; Williams, Gary W.; Wright, Adam; Yook, Karen; Berriman, Matthew; Kersey, Paul J.; Schedl, Tim; Stein, Lincoln; Sternberg, Paul W.

doi:10.1093/nar/gkx998

Cited by 182 publications

(180 citation statements)

References 17 publications

(17 reference statements)

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“…Scaffolds shorter than 500 bp were discarded prior to annotation. Wormbase version WS264 of the C. elegans genome was used (Lee et al 2018). ‡ BUSCO does not find core genes in the complete C. elegans N2 genome.…”

Section: Caenorhabditis Speciesmentioning

confidence: 99%

Comparative genomics of 10 newCaenorhabditisspecies

et al. 2019

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The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis , many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole‐genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

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Section: Caenorhabditis Speciesmentioning

confidence: 99%

Comparative genomics of 10 newCaenorhabditisspecies

et al. 2019

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“…Thus far, data in ProtaBank has come directly from the published literature and has been manually entered by ProtaBank developers. To aid in the future data collection process, ProtaBank is designed to accept data input directly from the researchers who performed the study, a strategy that has proved effective in populating other biological databases such as the PDB, GenBank, ArrayExpress, and WormBase . Any user can input a study via the ProtaBank data submission tools.…”

Section: Database Construction and Contentmentioning

confidence: 99%

“…To aid in the future data collection process, ProtaBank is designed to accept data input directly from the researchers who performed the study, a strategy that has proved effective in populating other biological databases such as the PDB, GenBank, ArrayExpress, 25 and WormBase. 26 Any user can input a study via the ProtaBank data submission tools. Two modes of data deposition are provided: an interactive web interface that supports upload of data in a spreadsheet format [i.e., via a comma-separated values (CSV) file] (see Supporting Information Fig.…”

Section: Data Deposition and Curationmentioning

confidence: 99%

ProtaBank: A repository for protein design and engineering data

et al. 2018

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We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user‐friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org.

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“…Many of these genes are C. elegans or nematode-specific, 356 however, some have homology to human genes of unknown function. WormBase also 357 aggregates microarray and RNA-seq information and annotates genes that respond to 358 pharmacological treatments (Lee et al 2018). We also used this information to 359 differentiate genes within Unknown: regulated by multiple stresses that respond to at 360 least two commonly used stressors.…”

Section: Elegans Gene Annotation 313mentioning

confidence: 99%