SyMAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SyMAP
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Tool usage distribution map

This map represents all the scientific publications referring to SyMAP per scientific context
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Associated diseases

This word cloud represents SyMAP usage per disease context
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Protocols

SyMAP specifications

Information


Unique identifier OMICS_11713
Name SyMAP
Alternative name Synteny Mapping and Analysis Program
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 4.2
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publications for Synteny Mapping and Analysis Program

SyMAP citations

 (91)
library_books

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

2018
PLoS One
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] ed alignments were then used to identify the locations of the centromere on each chromosome based on the genetic map produced by [].To identify duplicated regions (homeologous) of the Chinook genome, SyMAP [] was used to align a masked version of the genome (see section 2.5) to itself and identify duplicated blocks using the following parameters: merge_blocks = 1, nucmer_only = 1, and mindots = 20 […]

library_books

Whole genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)

2018
Sci Rep
PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] Using SyMAP vers. 4.2 we analyzed the collinearity of gene order at the whole chromosome scale (i.e. macrosynteny as per Hane et al.) between the Pearlscale Pygmy Angelfish C_vrolikii_CAS243847_v1.0 and the […]

library_books

PhyloChromoMap, a Tool for Mapping Phylogenomic History along Chromosomes, Reveals the Dynamic Nature of Karyotype Evolution in Plasmodium falciparum

2018
Genome Biol Evol
PMCID: 5800058
PMID: 29365145
DOI: 10.1093/gbe/evy017

[…] We perform a synteny analysis of subtelomeric and internal young portions using SyMAP (; , online). We explore different values for the minimum number of anchors to define a synteny block (i.e., from 3 to 7) and do not see any major differences (, online). We choose parameters […]

library_books

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

2018
BMC Genomics
PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] 12X.v2) were grouped into a chromosome 21. Synteny blocks between the genome assemblies of V. vinifera ‘Sultanina’ (AP, PLAT_d, MERGE, and PLAT*_GC) and V. vinifera (PN40024 12X.v2) were computed by SyMAP []. SyMAP provides the number of anchors have alignment lengths >10 kb with the reference genome. All four assemblies were separately mapped with V. vinifera using the promer option of MUMmer [] […]

library_books

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees

2018
PLoS One
PMCID: 5755769
PMID: 29304093
DOI: 10.1371/journal.pone.0189738

[…] d reciprocal best hit BLAST searches. In our comparative study, we could not include Crithidia mellificae/Lotmaria passim ([,], as the protein database is not available.Synteny analysis was done with SyMap, version 4.2 []. The genome assembly of each species was loaded into SyMap using a minimum contig length threshold of 2000 bp. Alignment and synteny analysis of C. bombi and C. expoeki versus al […]

library_books

Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

2017
Sci Rep
PMCID: 5741766
PMID: 29273719
DOI: 10.1038/s41598-017-18374-y

[…] Synteny was evaluated via SyMAP and progressive MAUVE algorithms using current L. infantum (v.9, GeneDB.org) and L. major genomes as reference. Synteny graphs were prepared by genoPlotR, and provided as Supplementary Figures  […]


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SyMAP institution(s)
BIO5 Institute, University of Arizona, Tucson, AZ, USA
SyMAP funding source(s)
This project is supported by the National Research Initiative of USDA's National Institute of Food and Agriculture, grant #0214643.

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