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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types.
The genome of the mesopolyploid crop species Brassica rapa
The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation
Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker
Genetic maps and the use of synteny.
This chapter demonstrates the application of online resources to identify candidate genes underlying a QTL, conduct genome comparisons, identify syntenic regions and view comparative genetic maps in grass and Brassica species.
Single nucleotide polymorphism discovery in barley using autoSNPdb.
Molecular markers are used to provide the link between genotype and phenotype, for the production of molecular genetic maps and to assess genetic diversity within and between related species. Single
Predicting polymorphic EST‐SSRs in silico
The characterization of barley EST‐SSRs and the identification of putative polymorphic SSRs from EST data are presented and redundancy of a polymorphism and co‐segregation with accessions are calculated.
Discovering genetic polymorphisms in next-generation sequencing data.
The recent advances in next-generation sequencing technology are described, together with preliminary approaches that can be applied for single nucleotide polymorphism discovery in plant species, to offer a means to identify and characterize the wealth of genetic polymorphisms underlying the vast phenotypic variation in biological systems.
Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS.
The results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.
Single nucleotide polymorphism discovery from wheat next-generation sequence data.
This work produced wheat transcriptome sequence data using 454 sequencing technology and applied this for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer, to identify 38 928 candidate SNPs.
AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants
An integrated SNP discovery pipeline is developed, which identifies SNPs from assembled EST sequences with high resolution in a custom relational database along with EST source and annotation information.