SyMAP pipeline

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


Maintainer


  • person_outline SyMAP Team <>

Publications for Synteny Mapping and Analysis Program

SyMAP IN pipelines

 (3)
2017
PMCID: 5741766
PMID: 29273719
DOI: 10.1038/s41598-017-18374-y

[…] new genes uncovered in the new assembled l. infantum genome. the complete annotation of the new genome (gff3 file) is provided in the supplementary fileĀ 1 in excel format., synteny was evaluated via symap45 and progressive mauve46 algorithms using current l. infantum (v.9, genedb.org) and l. major 24 genomes as reference. synteny graphs were prepared by genoplotr47, and provided as supplementary […]

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

[…] and maize (ftp://ftp.genome.arizona.edu) was downloaded. synteny mapping and analysis program v4.0 (symap) [47] was used to generate the syntenic relationship with rice and maize. symap uses mummer [48] program for alignment purpose and passes through four phases (alignment, anchor clustering, […]

2013
PMCID: 3878662
PMID: 24341590
DOI: 10.1186/1471-2164-14-883

[…] not assembled completely (tableĀ 4), the numbers of paired-end bess potentially collinear with target genomes could be higher than detected., in order to detect large syntenic regions, we used the symap [23] program based on the bess embedded in the contigs to anchor uv-8b phaseia contigs to the genomes of m. anisopliae, t. reesei, n. haematococca and c. militaris. under the symap default […]

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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