Tools

DTScreen Genome-scale screening tool for drug targets identification
DTscreen v1 is a user-friendly and free bioinformatics tool, was developed for facilitating any researchers in biomedical field to perform a genome-scale screening for identifying all attractive drug targets against pathogenic diseases. The proposed drug targets were reported based on 1) non-homolog with human proteins in term of protein signatures and 2) gene essentiality reported from a large-scale wet experiment
The tool was constructed in Visual Basic language and implemented as an application platform. DTscreen provides a fast and automated performance for identifying drug targets in the three model pathogenic bacteria, including Salmonella typhi CT18, Mycobacterium tuberculosis H37Rv and Escherichia coli K12-MG1655. Fortunately, users can apply DTscreen v1 to other interested pathogens by inserting required biological information of each pathogen.
Developer team
Arporn Juntrapirom
Saowalak Kalapanulak, Ph.D.
Treenut Saithong, Ph.D.
S. Kalapanulak, A. Juntrapirom, T. Saithong (2012) DTscreen v1: A Novel Drug Targets Identification Tool for Pathogenic Diseases Through Protein Signature-based Approach. Proceedings of The 23rd Annual Meeting
of the Thai Society for Biotechnology “Systems Biotechnology: Quality & Success” (TSB2011), 1-2 February 2012, The Imperial Queen’s Park Hotel, Bangkok, Thailand.
DTScreeen is available on request.download
Vanted carbon assimilation v1 Cassava metabolic pathway
The reconstructed pathway can be used as a template to facilitate the omics data integration into the metabolic pathways. This cassava carbon assimilation pathway includes cell wall biosynthesis, starch biosynthesis, and respiration pathways.
This work was presented in the Conference on Computational Systems-Biology and Bioinformatics (CSBio 2012), 3-5 October 2012, Centara Grand at Central Plaza Ladprao, Bangkok, Thailand in title of “Transcriptomic data integration inferring the dominance of starch biosynthesis in carbon utilization of developing cassava roots”, and was published in Elsevier Procedia Computer Science open access. Regarding the research work, the three key carbon metabolism pathways—cell wall biosynthesis, starch biosynthesis, and respiration pathway—were reconstructed following the protocol of Rongsirikul et al., 2010. In brief, the cassava metabolic pathways were reconstructed through comparative genomics approach (reciprocal BLASTp) using multiple plant templates: Arabidopsis, rice, maize, castor bean, and potato. The supplemental data infers the carbon partitioning during cassava root development at the transcriptional level—fibrous root (FR), developing storage root (DR), and mature storage root (MR) from Yang et al., 2011—was provided as the Appendix A.
Developer team
Wanatsanan Siriwat
Treenut Saithong, Ph.D.
Saowalak Kalapanulak, Ph.D.
Siriwat W, Kalapanulak S, Suksangpanomrung M, Netrphan S, Meechai A, Saithong T., 2012 “Transcriptomic data integration inferring the dominance of starch biosynthesis in carbon utilization of developing cassava roots,” 3rd International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2012), Bangkok, Thailand.
Vanted carbon assimilation v1 is available on request.download
Metabolic pathways of starch biosynthesis in cassava
The metabolic pathway of starch biosynthesis in cassava, including carbon dioxide fixation (Calvin cycle), sucrose synthesis and storage starch synthesis, were reconstructed based on the comparative genomics approach. The cassava genes comprised of the starch biosynthesis pathway were identified from their orthologues presented in the five template plants (i.e. Arabidopsis, rice, maize, castor bean, and potato). There constructed pathways were presented in both SmartDraw (an informative format of the pathway map) and VANTED (an interactive format of the pathway map for omics data integration) platforms. The reconstructed pathway maps and the other supplemental data of this work are ready to download.
*Treenut Saithong, Oratai Rongsirikul, Saowalak Kalapanulak,Porntip Chiewchankaset, Wanatsanan Siriwat, Supatcharee Netrphan, Malinee Suksangpanomrung, Asawin Meechai, Supapon Cheevadhanarak
*To whom correspondence
 Metabolic pathways of starch biosynthesis in cassava are available on request.download
Tools in Arthrospira research Tools are available at the Arthrospira website.