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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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  • person_outline SynFind <>

Information


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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Publication for SynFind

SynFind in pipeline

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

[…] , http://tree.bio.ed.ac.uk/software/figtree/ , http://chibba.agtec.uga.edu/duplication/index/downloads , http://genomevolution.org/coge/synmap.pl , https://genomevolution.org/coge/synfind.pl , http://banana-genome.cirad.fr , http://bar.utoronto.ca/ , the supplementary material for this article can be found online at: […]

SynFind in publications

 (14)
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 […]

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 […]

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 […]

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 […]

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 […]

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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