SyMAP protocols

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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

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Documentation


Publications for Synteny Mapping and Analysis Program

SyMAP in pipelines

 (12)
2017
PMCID: 5225507
PMID: 28073340
DOI: 10.1186/s12864-016-3457-9

[…] length of the query sequence p and l h denotes the length of the sequence that was selected as the best hit among annotations produced by the other method., genome synteny was analyzed by using the synteny mapping and analysis program (symap) v4.2 [] and default parameters. colletotrichum sublineola scaffolds were aligned to the 13 previously published chromosomes of c. graminicola strain […]

2017
PMCID: 5467034
PMID: 28368449
DOI: 10.1093/gigascience/gix023

[…] were used to construct a phylogenetic tree by mrbayes []. the divergence time was estimated using the software multidivtime []. colinearity between d. longan and p. trichocarpa was computed by symap v3.4 []. subsequently, tf families were identified using the ipr2genomes tool in greenphyldb v. 2.0 [] based on interpro domains, and gene family expansion and contraction within […]

2017
PMCID: 5472924
PMID: 28619070
DOI: 10.1186/s12864-017-3850-z

[…] tree was drawn using figtree v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). scaffolds of finger millet genome was concatenated and syntenic relationship among poaceae species was inferred by symap tool []. protein sequences of plant transcription factors (tfs) were retrieved from plant transcription factor database (http://planttfdb.cbi.pku.edu.cn/index.php) and used as a reference […]

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

[…] e new genes uncovered in the new assembled l. infantum genome. the complete annotation of the new genome (gff3 file) is provided in the supplementary file  in excel format., 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  […]

2016
PMCID: 4739524
PMID: 26840746
DOI: 10.1371/journal.pone.0148453

[…] pseudomolecules build 7.0 (ftp://ftp.plantbiology.msu.edu/pub/data/eukaryotic_projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/) and maize (ftp://ftp.genome.arizona.edu) was downloaded. synteny mapping and analysis program v4.0 (symap) [] was used to generate the syntenic relationship with rice and maize. symap uses mummer [] program for alignment purpose and passes through four […]


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SyMAP in publications

 (75)
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] 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 = […]

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

[…] to the mitos web server to validate its annotations (http://mitos.bioinf.uni-leipzig.de). the mitos annotation confirmed 2 rrnas, 13 coding genes and 22 trnas (table )., a synteny analysis using symap vers. 4.2, revealed 372 total shared syntenic blocks with 100 inverted, representing 92% of the centropyge vrolikii and 90% of the nile tilapia (oreochromis niloticus) contig lengths […]

PMCID: 5800058
PMID: 29365145
DOI: 10.1093/gbe/evy017

[…] (; ). in chromosome 10 this region is less obvious, encompassing only around 1 kb with a 94% gc content (, online)., 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 […]

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 […]

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

[…] is encoded by a single exon, and a very similar distribution of exons per gene altogether. furthermore, there is a high degree of synteny between the two species as shown in . quantitatively, the symap synteny analysis revealed 5,098 anchors in 99 syntenic blocks with conserved gene order among c. bombi and c. expoeki []. of these conserved blocks, 18 are smaller than 100 kbp, 80 blocks […]


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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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