ArticleBMC bioinformatics2008
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic 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 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.BMC genomics · 2025Article
- Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters.NAR genomics and bioinformatics · 2024Article
- FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation.Bioinformatics (Oxford, England) · 2021Article
- Tasks, Techniques, and Tools for Genomic Data Visualization.Computer graphics forum : journal of the European Association for Computer Graphics · 2019Article
- OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.Genomics, proteomics & bioinformatics · 2017Article
- GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm.BMC evolutionary biology · 2016Article
- Strategic genome-scale prioritization of unique drug targets: A case study of Streptococcus gordonii.Bioinformation · 2013Article
- In silico synteny based comparative genomics approach for identification and characterization of novel therapeutic targets in Chlamydophila pneumoniae.Bioinformation · 2013Article
- Positional orthology: putting genomic evolutionary relationships into context.Briefings in bioinformatics · 2011Review
- Identification of mammalian orthologs using local synteny.BMC genomics · 2009Article
- The Microbe browser for comparative genomics.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.
resultsAfter comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.
conclusionSynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.
Indexed as
Identifiers
What OpenQuestion holds
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.