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SynFind specifications

Information


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

Documentation


Maintainer


  • 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 citations

 (16)
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

[…] 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 re […]

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

[…] ynmap 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 excelsio […]

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

[…] depending 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 from our QTLs. […]

call_split

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
call_split See protocol

[…] gene 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. […]

library_books

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

2016
Sci Rep
PMCID: 5120318
PMID: 27876851
DOI: 10.1038/srep37536

[…] gans and Brugia malayi. Synteny was assessed on scaffolds >1 Mb using pairwise alignments with E-value < 10−6 and homologous regions were visualized using CIRCOS. Macro-synteny was analysed using the SynFind and SynMap tools from CoGe. […]

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

[…] eater 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 da […]

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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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