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SynFind specifications

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Unique identifier OMICS_11712
Name SynFind
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

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Unique identifier OMICS_11712
Name SynFind
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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SynFind citations

 (14)
library_books

A tutorial of diverse genome analysis tools found in the CoGe web platform using Plasmodium spp. as a model

2018
PMCID: 5887277
DOI: 10.1093/database/bay030

[…] closely related species () and to study the role of duplications on evolutionary adaptation and innovation (). coge’s tools can be used to explore these unique patterns in gene content evolution., synfind () can identify the location of regions syntenic to a query gene, the syntenic depth (number of times a region is syntenic to target genome regions) and the number of genes in each syntenic […]

library_books

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo and autopolyploidization events

2018
BMC Biol
PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] was used to compare the olive genome against itself using the syntenic path assembly option [] and to remove scaffolds without conserved synteny (see additional file : figure s1). then, we used synfind to obtain the syntenic depth, which is the number of conserved syntenic regions between the query genome and a reference. we obtained this value for comparisons of the olive, fraxinus […]

library_books

Flowering Locus C (FLC) Is a Potential Major Regulator of Glucosinolate Content across Developmental Stages of Aethionema arabicum (Brassicaceae)

2017
Front Plant Sci
PMCID: 5445170
PMID: 28603537
DOI: 10.3389/fpls.2017.00876

[…] on the qtl location (e.g., q1.2 would be the second qtl found on linkage group 1)., assessed the homology of all gs pathway genes between a. thaliana and the ae. arabicum v1 genome. we used synfind () and the ae. arabicum v2.5 genome in coge (nguyen et al., in preparation; ) to establish if any of the homologs found by of the gs pathway occur between a one marker-interval […]

library_books

Lineage Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening

2016
Front Plant Sci
PMCID: 5133247
PMID: 27994606
DOI: 10.3389/fpls.2016.01778

[…] identifiers along the chromosomes using an in house-script. syntenic blocks from the pgdd and published data were used to identify wgd-derived genes for plant species other than banana (; ; ; ). synfind was used for synteny search at specific regions between species., plant materials corresponded to an experimental setting that was previously described in . banana fruits of the cavendish […]

library_books

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

2016
Genome Biol
PMCID: 5084476
PMID: 27793170
DOI: 10.1186/s13059-016-1080-3

[…] than one in at least one segment of any replicate. correlation matrices and heat map visualizations were constructed using r software packages (code available upon request). coge blast and coge synfind tools were used to find core c4 gene and tf orthologs for the different grass species [, ]. segments 1, 4, 9, and 14 from z. mays and 1, 3, 6, and 9 from o. sativa from previously published […]

library_books

Functional conservation and diversification of the soybean maturity gene E1 and its homologs in legumes

2016
Sci Rep
PMCID: 4942777
PMID: 27405888
DOI: 10.1038/srep29548

[…] of the segmental duplication event was performed using the formula, t  =  ks/2λ, in which the mean synonymous substitution rate (λ) was set to 6.1 × 10−9 based on previous report for fabaceae., the synfind and gevo tools at coge online server (https://genomevolution.org/coge/index.pl) were used for microsyntenic analysis. the segment (pac.26299773), which represents a region that contained […]


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SynFind institution(s)
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
SynFind funding source(s)
The Fujian provincial government for a Fujian “100 Talent Plan” award; the Gordon and Betty Moore Foundation grant number 3383; the National Science Foundation grant number DBI – 1265383. iPlant is supported by the National Science Foundation under grant numbers DBI-0735191 and DBI-1265383.

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