SynMap specifications

Information


Unique identifier OMICS_13395
Name SynMap
Interface Web user interface
Restrictions to use None
Input data Putative genes or regions of homology between two genomes
Output data Log file, homolog search, diagonals and results.
Programming languages Python
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • FractBias

Documentation


Maintainer


  • person_outline Eric Lyons <>

Additional information


https://genomevolution.org/wiki/index.php/FractBias

Information


Unique identifier OMICS_13395
Name SynMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Putative genes or regions of homology between two genomes
Output data The graphical output of FractBias is composed of subplots for each target genome chromosome.
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • FractBias

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Eric Lyons <>

Additional information


https://genomevolution.org/wiki/index.php/FractBias

SynMap articles

SynMap citations

 (2)
2015
PMCID: 4404975

[…] match/mismatch scores, 1/-2. microsyntenic blocks were visualized using the web-based genome synteny viewer (revanna et al., 2011). the synmap analysis tool was used (https://genomevolution.org/coge/synmap.pl) to determine if identified syntenic loci were located in large conserved blocks of m. truncatula, l. japonicus, c. arietinum, g. max, p. vulgaris, and c. cajan genomes. sequences […]

2013
PMCID: 3621523

[…] and plant expression vectors, pexsg-yfp-gw, with gateway technology., to identify the intra-genome (g. max) or cross-genome (g. max and m. truncatula) syntenic relationships we employed, synmap (http://genomevolution.org/coge/synmap.pl). to investigate the synteny of blocks containing pht1 genes, homology data derived from cds–cds comparisons made using blastz, with an e-value cutoff […]

SynMap institution(s)
BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA; Genetis GIDP, University of Arizona, Tucson, AZ, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
SynMap funding source(s)
This work has been supported by the U.S. National Science Foundation (IOS – 1339156 and IOS – 1444490).

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