Seq-SNPing specifications

Information


Unique identifier OMICS_14874
Name Seq-SNPing
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.21
Stability No
Maintained No

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Publication for Seq-SNPing

Seq-SNPing citations

 (2)
library_books

Single nucleotide polymorphism barcoding of cytochrome c oxidase I sequences for discriminating 17 species of Columbidae by decision tree algorithm

2017
Ecol Evol
PMCID: 5496562
PMID: 28690801
DOI: 10.1002/ece3.3045

[…] pecies for above applications. Here, we show the development of a minimal set of SNP markers that is robust enough to fingerprint a diverse collection of species. In our previously developed software Seq‐SNPing (Chang et al., ), the SNPs were easy to identify after sequence alignment.In this article, we propose a decision tree‐based SNP barcoding (DTSB) algorithm that automatically generates barco […]

library_books

Conserved PCR Primer Set Designing for Closely Related Species to Complete Mitochondrial Genome Sequencing Using a Sliding Window Based PSO Algorithm

2011
PLoS One
PMCID: 3060828
PMID: 21445268
DOI: 10.1371/journal.pone.0017729

[…] onsidering the situations in multi-sequence alignment, and for the circular sequences like the mt genome. In contrast, some sequence alignment tools, such as CLUSTALW , TBA , MAVID , MLAGAN , Pecan , Seq-SNPing , AQUA , and Cgaln , were developed without a primer design function. Accordingly, the development of integrated algorithms for designing feasible primer sets for entire mt genome sequences […]

Seq-SNPing institution(s)
Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, China; Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, China; Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, China; Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan, China; Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan, China
Seq-SNPing funding source(s)
This work is supported by the National Science Council in Taiwan under grants 97-2622-E-151-008-CC2, NSC96-2221-E-214-050-MY3, NSC96-2622-E214-004-CC3, 96- 2622-E-151-019-CC3, NSC95-2622-E-214-004-CC3, and grant KMU-EM-97-1.16.

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