SyMAP protocols

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description
SyMAP computational protocol

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

 (13)
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 [134] and default parameters. colletotrichum sublineola scaffolds were aligned to the 13 previously published chromosomes of c. graminicola strain […]

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

[…] 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 [134] and default parameters. colletotrichum sublineola scaffolds were aligned to the 13 previously published chromosomes of c. graminicola strain m1.001 [69]., fungal protein sequences […]

2017
PMCID: 5432662
PMID: 28540183
DOI: 10.1016/j.gdata.2017.05.007

[…] reads were merged with pandaseq and assembled de novo using newbler software. genes were predicted by fgenesh and annotated using blastx against the ncbi non-redundant protein database. we used symap for pairwise synteny mapping and allmaps to integrate our draft genome with a rad-snp-based genetic map of c. olitorius. consent n/a sample source location barrackpore, kolkata, india […]

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 [30]. 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

[…] 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 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 […]

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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