scholarly journals Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0131925 ◽  
Author(s):  
Francesca Bertolini ◽  
Concetta Scimone ◽  
Claudia Geraci ◽  
Giuseppina Schiavo ◽  
Valerio Joe Utzeri ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Sequence Data ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Single Nucleotide ◽  
Comparative Sequence ◽  
Horse Genome ◽  
Equus Asinus

Status and future perspectives of single nucleotide polymorphisms (SNPs) markers in farmed fishes: Way ahead using next generation sequencing

Gene Reports ◽  
2017 ◽  
Vol 6 ◽  
pp. 81-86 ◽  
Author(s):  
Kiran Dashrath Rasal ◽  
Vemlawada Chakrapani ◽  
Amrendra Kumar Pandey ◽  
Avinash Rambhau Rasal ◽  
Jitendra K. Sundaray ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Future Perspectives ◽  
Single Nucleotide ◽  
Generation Sequencing

scholarly journals Mining for single nucleotide polymorphisms in pig genome sequence data

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 4 ◽  
Author(s):  
Hindrik HD Kerstens ◽  
Sonja Kollers ◽  
Arun Kommadath ◽  
Marisol del Rosario ◽  
Bert Dibbits ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
Sequence Data ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Sequence Data ◽  
Pig Genome

scholarly journals An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms

2007 ◽  
Vol 2007 ◽  
pp. 1-7 ◽  
Author(s):  
B. Jayashree ◽  
Manindra S. Hanspal ◽  
Rajgopal Srinivasan ◽  
R. Vigneshwaran ◽  
Rajeev K. Varshney ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Sequence Data ◽  
Snp Genotyping ◽  
Model Organisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Web Interfaces

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

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