SynMap protocols

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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

 (11)
2018
PMCID: 5940132
PMID: 29519939
DOI: 10.1534/g3.117.300443

[…] were hard masked using ncbi windowmasker () and genome-wide alignments were calculated with last (). from these alignments, a genome-scale dotplot indicating syntenic regions was generated using synmap (; )., the colliv2 assembly is currently unannotated. therefore, to compare gene content between assemblies, we estimated the number of annotated cliv_2.1 genes absent from colliv2 based […]

2017
PMCID: 5604175
PMID: 28927400
DOI: 10.1186/s12915-017-0419-x

[…] isoform. maximum likelihood trees were constructed based on the concatenated alignments of 2381 orthologous protein-coding genes using raxml 8.2.8 [] with a jtt + γ model and 1000 bootstraps., synmap [] using blastz [] alignments, dagchainer [] (options -d 30 and -a 2), and no merging of syntenic blocks were used as part of the coge platform [] to identify syntenic blocks […]

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

[…] is 1 × 10−8 as calculated elsewhere 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 synmap 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 20. […]

2016
PMCID: 4987669
PMID: 27531320
DOI: 10.1038/srep31586

[…] number prjna312694, and the gene annotation used for the analyses were provided to the banana genome hub (banana-genome-hub.southgreen.fr/organism/musa_itinerans)., using the web-based tool synmap on the plant comparative genome platform coge (https://genomevolution.org/coge/), the syntenic regions between m. itinerans and m. acuminata were generated, and scaffolds or contigs of m. […]

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: […]


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SynMap in publications

 (71)
PMCID: 5954274
PMID: 29764371
DOI: 10.1186/s12864-018-4462-y

[…] the processes of whole genome duplication and fractionation compound inherent inferential difficulties due to genome rearrangement. a telling aspect in the widely-used synteny block identifier synmap [, ] is the default requirement that at least five pairs of orthologous genes in two genomes or five pairs of paralogous genes in a single genome, in close succession, are necessary […]

PMCID: 5887277
DOI: 10.1093/database/bay030

[…] coge’s provides powerful tools for exploring changes in genome structure and sequence evolution across multiple species, and making inferences on the evolutionary mechanisms and forces behind them., synmap (, ) was used to identify large-scale changes in genome organization amongst plasmodium species (). specifically, whole genome pairwise comparisons were performed using default synmap […]

PMCID: 5887293
PMID: 29617811
DOI: 10.1093/gbe/evy061

[…] selective constraint even in present day populations, but that this pattern of constraint was nonetheless intrinsic to them prior to polyploidy., we obtained pairs of at-α duplicates using coge’s synmap algorithm () and merged this list with the at-α duplicates reported by using version 10.02 of the arabidopsis thaliana col-0 genome as our reference (). we excluded from our ohnolog lists […]

PMCID: 5802725
PMID: 29423238
DOI: 10.1038/s41438-017-0013-y

[…] of these interactions is directly proportional to chromosome length. therefore the median trans percentage values were extracted from overall values., syntenic dot plots were generated with synmap using last for whole-genome comparisons. a minimum of five synteny genes with a maximum distance of 50 kb between adjacent genes was used to seed a syntenic block. syntenic gene pairs […]

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

[…] olive and oleaster and, hence, must have predated the domestication of the species. this is confirmed when using the number of synonymous substitutions per synonymous site (ks) values predicted by synmap when comparing the two o. europaea genomes. the ks graph provided by synmap presents five peaks (see additional file : figure s11c). the first is formed by proteins that were identical […]


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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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