ArticleBMC research notes2010
Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0.
Article in BMC research notes, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- An Analysis of Adenovirus Genomes Using Whole Genome Software Tools.Bioinformation · 2016Article
- Comparative analysis of multiple inducible phages from Mannheimia haemolytica.BMC microbiology · 2015Article
- Genome rearrangements can make and break small RNA genes.Genome biology and evolution · 2015Article
- Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids.BMC genomics · 2014Article
- Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria.BMC genomics · 2013Article
- CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes.BMC research notes · 2013Article
- The sub-cellular localization of Sulfolobus DNA replication.Nucleic acids research · 2012Article
- Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs.Journal of biosciences · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling.
findingsGeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations.
conclusionsThe web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.
Identifiers
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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.