ArticleBMC bioinformatics2008
JCoast - a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed.
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- Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.Microbial ecology · 2017Article
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- Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions.Frontiers in microbiology · 2016Article
- Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria.Nature · 2015Article
- Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.eLife · 2015Article
- Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803.The ISME journal · 2014Article
- ITEP: an integrated toolkit for exploration of microbial pan-genomes.BMC genomics · 2014Article
- The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides.Applied and environmental microbiology · 2013Article
- Metabolic engineering of Bacillus subtilis for growth on overflow metabolites.Microbial cell factories · 2013Article
- The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis.Environmental microbiology · 2013Article
- Ecology of marine Bacteroidetes: a comparative genomics approach.The ISME journal · 2013Article
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- Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrent sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions.
resultsThe JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets.
conclusionJCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.
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Registered trials
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.