DRIMM-Synteny statistics

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DRIMM-Synteny specifications

Information


Unique identifier OMICS_11707
Name DRIMM-Synteny
Alternative name Duplications and Rearrangements In Multiple Mammals-Synteny
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Son K. Pham

Publication for Duplications and Rearrangements In Multiple Mammals-Synteny

DRIMM-Synteny citations

 (3)
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Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.)

2017
Front Plant Sci
PMCID: 5694560
PMID: 29184557
DOI: 10.3389/fpls.2017.01843

[…] son et al., ) genomes. The blastn alignment of 40,267 mapped markers from the wheat consensus SNP map published by Wang et al. () and AGK genes, delivered orthologs between these two resources. Using DRIMM-Synteny tool (Pham and Pevzner, ), we built synteny groups allowing the identification of ancestral regions as well as the ancestral gene content and order between wheat markers along the consen […]

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Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events

2015
BMC Genomics
PMCID: 4603330
PMID: 26449933
DOI: 10.1186/1471-2164-16-S10-S8

[…] here are many programs designed to find synteny (or syntenic) blocks in the comparison of two or more eukaryotic gene orders, e.g., i-ADHoRe [], DAGchainer [], Cinteny[], CYNTENATOR [], MCScan [] and DRIMM-Synteny []. These differ in search strategy, flexibility, performance and interpretation. SynMap is based on the DAGchainer algorithm, and balances sensitivity with rigour in finding blocks. It […]

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Evaluating synteny for improved comparative studies

2014
Bioinformatics
PMCID: 4058928
PMID: 24932010
DOI: 10.1093/bioinformatics/btu259

[…] n homologies. We discuss how the quality of SBs can be measured against this definition and illustrate our approach with a comparison of three current tools for the construction of SBs—Cyntenator (), DRIMM-Synteny () (DRIMM) and i-ADHoRE 3.0 () (i-ADHoRe). We investigate the underlying heuristics and evaluate the results on a dataset of eight full genomes of various species of yeasts from the Yeas […]


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DRIMM-Synteny institution(s)
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
DRIMM-Synteny funding source(s)
The project was financially supported by the Vietnam Education Foundation fellowship.

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