ArticleGenome biology and evolution2015
SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- De novo discovery of conserved gene clusters in microbial genomes with Spacedust.Nature methods · 2025Article
- Genome-Wide Identification and Expression of NF-YC Transcription Factors in Blueberry Under Abiotic Stress Conditions.International journal of molecular sciences · 2025Article
- Arabidopsis as a model for translational research.The Plant cell · 2025Review
- AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.Briefings in bioinformatics · 2024Article
- Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry.Horticulture research · 2023Article
- Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes.Nucleic acids research · 2023Article
- A cryptic natural variant allele of BYPASS2 suppresses the bypass1 mutant phenotype.Plant physiology · 2023Article
- The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae.The Plant cell · 2023Article
- Tracing the Evolution of thePlants (Basel, Switzerland) · 2022Article
- Tracking of Diversity and Evolution in the Brown Rot FungiFrontiers in microbiology · 2022Article
- Evolutionary history and pan-genome dynamics of strawberry (Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Origin and Fates ofInternational journal of molecular sciences · 2021Article
- Abundant expression of maternal siRNAs is a conserved feature of seed development.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Transcriptomic and Phenotypic Analysis of aFrontiers in microbiology · 2020Article
- Independent Recruitment of Duplicated β-Subunit-Coding NAD-ME Genes Aided the Evolution of C4 Photosynthesis in Cleomaceae.Frontiers in plant science · 2020Article
- The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae).Genome biology and evolution · 2019Article
- Comparative Analysis ofInsects · 2019Article
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6 authors.
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Abstract
The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity for studying gene loss and gene transposition. However, the identification of syntenic regions requires complex analyses which must be repeated for pairwise comparisons between any two species. Therefore, as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of target genomes. SynFind is capable of reporting per-gene information, useful for researchers studying specific gene families, as well as genome-wide data sets of syntenic gene and predicted gene locations, critical for researchers focused on large-scale genomic analyses. Inference of syntenic homologs provides the basis for correlation of functional changes around genes of interests between related organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism. SynFind makes use of a powerful job execution framework that promises scalability and reproducibility. SynFind can be accessed at http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
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