SynMap protocols

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

Publications for SynMap

SynMap IN pipelines

 (5)
2018
PMCID: 5940132
PMID: 29519939
DOI: 10.1534/g3.117.300443

[…] (morgulis et al. 2006) and genome-wide alignments were calculated with last (kielbasa et al. 2011). from these alignments, a genome-scale dotplot indicating syntenic regions was generated using synmap (lyons and freeling 2008; lyons et al. 2008)., the colliv2 assembly is currently unannotated. therefore, to compare gene content between assemblies, we estimated the number of annotated […]

2016
PMCID: 4726258
PMID: 26786968
DOI: 10.1038/srep19427

[…] 1 × 10−8 as calculated elsewhere76 for host-encoded genes and adjusted for the higher evolution rate of tes compared with genes., syntenic genes between artichoke and lettuce were identified using synmap77 on the coge platform (http://genomevolution.org) using last aligner (c-score filter = 0.4) and retrieving syntenic blocks with dagchainer adopting the following parameters: -d 10 -a 3 -dm […]

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

[…] , http://www.greenphyl.org/cgi-bin/index.cgi , 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: […]

2015
PMCID: 4404975
PMID: 25954293
DOI: 10.3389/fpls.2015.00268

[…] 8; gap existence cost, 5; gap elongation cost, 2; nucleotide 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, […]

2015
PMCID: 4404975
PMID: 25954293
DOI: 10.3389/fpls.2015.00268

[…] 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 […]

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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