ArticleBioinformatics (Oxford, England)2014
Comparative assembly hubs: web-accessible browsers for comparative genomics.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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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.
The trial behind it
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
15 citing papers in PubMed.
- Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.Genome research · 2023Article
- The UCSC Genome Browser database: 2022 update.Nucleic acids research · 2022Article
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- Whole-Genome Alignment and Comparative Annotation.Annual review of animal biosciences · 2019Review
- Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.GigaScience · 2018Article
- Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.Genome research · 2018Article
- Coordinate systems for supergenomes.Algorithms for molecular biology : AMB · 2018Article
- Computational pan-genomics: status, promises and challenges.Briefings in bioinformatics · 2018Review
- Transposable Element Genomic Fissuring inFrontiers in genetics · 2018Article
- WormBase 2016: expanding to enable helminth genomic research.Nucleic acids research · 2016Article
- PGD: a pangolin genome hub for the research community.Database : the journal of biological databases and curation · 2016Article
- Navigating protected genomics data with UCSC Genome Browser in a Box.Bioinformatics (Oxford, England) · 2015Article
- The UCSC Genome Browser database: 2015 update.Nucleic acids research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
motivationResearchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers.
resultsWe introduce a pipeline to easily generate collections of Web-accessible UCSC Genome Browsers interrelated by an alignment. It is intended to democratize our comparative genomic browser resources, serving the broad and growing community of evolutionary genomicists and facilitating easy public sharing via the Internet. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications. To demonstrate this work, we create a comparative assembly hub containing 57 Escherichia coli and 9 Shigella genomes and show examples that highlight their unique biology. AVAILABILITY AND IMPLEMENTATION: The source code is available as open source at: https://github.com/glennhickey/progressiveCactus The E.coli and Shigella genome hub is now a public hub listed on the UCSC browser public hubs Web page.
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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.