FSTVAL: a new web tool to validate bulk flanking sequence tags.
BACKGROUND
Information about a transgene locus is one of the major concerns in transgenic research because expression of the transgene or a gene interrupted by the integration event could be affected. Thus, the flanking sequences obtained from transgenic plants need to be analyzed in terms of genomic context, such as genic and intergenic regions. This process may consist of several steps: 1) elimination of a vector sequence from the flanking sequence, 2) finding the locations in the target genome, and 3) statistics of the integration sites. These steps could be automated for flanking sequences from several dozens of transgenic plants generated in an ordinary targeted gene expression strategy. It would be indispensable in a genome-wide mutagenesis screen using T-DNA or transposons because these projects often generate several thousands of transgenic lines and just as many loci of the transgene among the transgenic plants.


RESULTS
We present an open access web tool, flanking sequence tags validator (FSTVAL), to manage bulk flanking sequence tags (FSTs). FSTVAL automatically evaluates the FSTs and finds the best mapping positions of the FST against a known genome sequence. The statistics, in terms of genic and intergenic regions, are presented as a table, a distribution map, and a frequency graph along the chromosomes. Currently, 17 plant genome sequences, including Arabidopsis thaliana, Oryza sativa, and Glycine max, are available as reference genomes. We evaluated the utility and accuracy of the tool with 5,144 rice FSTs. The whole process, from uploading the sequences to generating tables of insertions, required a few minutes, with less than 4 clicks in the web environment.


CONCLUSIONS
Run for 1 year and tested over 1,000 times, we have confirmed FSTVAL efficiently handles bulk FSTs. FSTVAL is freely available without login at http://bioinfo.mju.ac.kr/fstval/.
Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, South Korea.
Joung Sug
JS
Kim
Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, South Korea.
Jiye
J
Kim
Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea.
Tae-Ho
TH
Lee
Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea.
Kyong Mi
KM
Jun
Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea.
Tea Hoon
TH
Kim
Upland Crop Research division, National Institute of Crop Science, Suwon, 441-857, South Korea.
Yul-Ho
YH
Kim
Upland Crop Research division, National Institute of Crop Science, Suwon, 441-857, South Korea.
Hyang-Mi
HM
Park
Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, South Korea.
Jong-Seong
JS
Jeon
Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, South Korea.
Gynheung
G
An
National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, South Korea.
Ung-Han
UH
Yoon
Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, South Korea.|Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea.
Baek Hie
BH
Nahm
Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea.
Yeon-Ki
YK
Kim