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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

 (79)
library_books

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

2018
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 = […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

call_split

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

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

[…] 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  […]


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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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