ArticleBMC bioinformatics2011
MicroSyn: a user friendly tool for detection of microsynteny in a gene family.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Analysis ofPlants (Basel, Switzerland) · 2023Article
- Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes.Nucleic acids research · 2023Article
- Comprehensive Genomic Survey, Structural Classification, and Expression Analysis of WRKY Transcription Factor Family in Rhododendron simsiiPlants (Basel, Switzerland) · 2022Article
- SWEET Transporters and the Potential Functions of These Sequences in Tea (Frontiers in genetics · 2021Article
- Systematic analysis of thePhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
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- A Chinese White Pear (Frontiers in plant science · 2020Article
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- Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering.Biomolecules · 2019Article
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- Genome-wide identification and comparative analysis of phosphate starvation-responsive transcription factors in maize and three other gramineous plants.Plant cell reports · 2018Article
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- Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar.Scientific reports · 2016Article
- Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants.Frontiers in genetics · 2016Article
- Article
- VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity.BioMed research international · 2016Article
- Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress.BMC genomics · 2015Article
- SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.Genome biology and evolution · 2015Article
- Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.Biology direct · 2015Article
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4 authors.
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Abstract
backgroundThe traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.
resultsWe introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: http://fcsb.njau.edu.cn/microsyn/.
conclusionsCase studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in Populus trichocarpa were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.
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