ArticleDatabase : the journal of biological databases and curation2017
Workflow and web application for annotating NCBI BioProject transcriptome data.
Article in Database : the journal of biological databases and curation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 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
4 citing papers in PubMed.
- Secondary analysis of the intestinal microbiota of healthy chickens.Poultry science · 2026Article
- Article
- Combining transcriptome analysis and GWAS for identification and validation of marker genes in thePeerJ · 2021Article
- Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments.Database : the journal of biological databases and curation · 2020Article
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Authors and funding
6 authors.
Funding
Abstract
Abstract: The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database: URL: http://www.ncbi.nlm.nih.gov/projects/physalis/.
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Registered trials
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