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WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations
journal: BMC Genomics
authors: Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S
year: 2007
links: http://bioinfo.biotec.or.th/WASP

Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results.

RESULTS: This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP. More...

The consolidation of Genome Databases

link: http://www.biotec.or.th/cogdb/
The consolidation of Genome Databases

Pan Asian SNP Database

link: http://www.biotec.or.th/PASNP
The aim of the project is to identify the different of Haplotype block between the population from Hapmap project (Caucasian and African) and the population from many countries in Pan Asian(include China, India, Indonesia, Japan, Korea, Malaysia, Phillippines, Singapore, Taiwan and Thai) .

Spirulina Project

link: http://spirulina.biotec.or.th
Spirulina platensis is a filamentous cyanobacterium belonging to the group of blue-green algae and performing oxygenic photosynthesis like higher plants. It is a very valuable microorganism. Its chemical composition includes protein (55%-70%), carbohydrates (15%-25%), essential fatty acids (18%) like linolenicacid (GLA), vitamins, minerals and pigments like carotenes, chlorophyll a and phycocyanin. The last one is used in food and cosmetic industries. S. platensis is considered as an excellent food, lacking toxicity and having corrective properties against viral attacks, anemia, tumor growth and malnutrition. It has been reported in literatures that the use of these microalgae as animal food supplement implies enhancement of the yellow in poultry and flamingos, growth acceleration, sexual maturation and increase of fertility in cattle.

Now Spirulina platensis c1 genome is sequencing. To become informative, these biological sequences are needed to be annotated, firstly by similarity search. Even if there are a lot of bioinformatics tools providing automatic genomic annotation, human judgment of such results is still required. To organize data from genome project and provide better access for scientists, it is an objective of this work to create monitoring and curation framework for Spirulina genome sequencing project. More..

Oil Palm DNA sequencing

We have developed several PCR-based microsattellite markers (SSLP markers) for identification of oil palm varieties. These markers can also use to facilitate the oil palm breeding program. Since most of the high yielding oil palm tree is the hybrid, SSLP markers are the most efficient technology for identifying the hybridity status from the seed and seedling. Now more than 50 SSLP markers for oil palm are available in our laboratory.

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