Bioinformatic Tools at Genome Institute

Bioinformatic tools and web-applications developed at the Genome Institute, BIOTEC

gelect: Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique

link: http://www4a.biotec.or.th/GI/tools/gelect

iNJclust framework: a genotypic data clustering software

link: http://www4a.biotec.or.th/GI/tools/injclust

METASEL: Free Karyotyping Tool using Gaussian-based Classification Technique

link: http://www4a.biotec.or.th/GI/tools/metasel

iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

link: http://www4a.biotec.or.th/GI/tools/iloci

microPIR and microPIR II (microRNA-Promoter Interaction Resource)

journal: PLoS ONE
authors: Piriyapongsa J, Bootchai C, Ngamphiw C, Tongsima S
year: 2012
link: www4a.biotec.or.th/micropir

journal: Database
authors: Piriyapongsa J, Bootchai C, Ngamphiw C, Tongsima S
year: 2014
link: www4a.biotec.or.th/micropir2

Rubber tree genome database

journal: DNA Research
authors: Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Chanprasert J, Ngamphiw C, Jomchai N, Therawattanasuk K, Tangphatsornruang S
year: 2011

link: www4a.biotec.or.th/rubber

Oil palm database

link: www4a.biotec.or.th/oilpalmdb

MUTANT : MUTation ANnotation Tool .

link: www4a.biotec.or.th/GI/tools/mutant

ipPCA : iterative pruning PCA for population structure study.

journal: BMC Bioinformatics
authors: Intarapanich A, Shaw P J, Assawamakin A, Wangkumhang P, Ngamphiw C, Chaichoompu K, Piriyapongsa J, and Tongsima S
year: 2009
link: http://www4a.biotec.or.th/GI/tools/ippca

RExPrimer : an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

journal: BMC Genomics
authors: Piriyapongsa J, Ngamphiw C, Assawamakin A, Wangkumhang P, Suwannasri P, Ruangrit U, Agavatpanitch G and Tongsima S
year: 2009
link: http://www4a.biotec.or.th/rexprimer

VarDetect

journal: BMC Bioinformatics
authors: Ngamphiw C, Kulawonganunchai S, Assawamakin A, Jenwitheesuk E and Tongsima S
year: 2008

The automate SNP detection software.

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
link: http://bioinfo.biotec.or.th/wasp

ThaiMUT DB : Thailand human mutation and variation database

journal: Human Mutation
authors: Ruangrit U, Srikummool M, Assawamakin A, Ngamphiw C, Chuechote S, Thaiprasarnsup V, Agavatpanitch G, Pasomsab E, Yenchitsomanas P, Mahasirimongkol S, Chantratita W, Palittapongarnpim P, Uyyanonvara B, Limwongse C, and Tongsima S
year: 2008
link: http://www4a.biotec.or.th/thaimut