FSTVAL

Introduction
Input and Processing
Output
Available organisms in the FSTVAL
Download FSTVAL

Although the huge number of genes has been predicted from the whole genome sequence information, functions of the most genes are still unknown. To determine a gene function, insertional mutagenesis by T-DNA or transposones has been generally used. FST-based insertion mutant databases of rice and Arabidopsis are freely available for searching a mutant in which they are interested (GABI-Kat, Salk Institute, FLAG, OTL). Additionally, large numbers of mutants still have been developed to obtain enough coverage of whole genomes. Flanking sequence of T-DNA or transposon from mutants must be recovered to confirm their positions along the chromosomes. The analysis inevitably involves a lot of processes which could be laborious and time-consuming.

Here, we have developed the Flanking Sequences Tag Validator (FSTVAL), a user friendly, first open access tool to manage bulk flanking sequences tag (FSTs) through the Web. The FSTVAL automatically evaluate the FSTs and find best mapping position of the FST against genome sequence, as well as graphical image and frequency graph are provided. Genome sequences of 16 plant organisms are available as references sequences.

There are two steps to analyze FSTs in FSTVAL; the first step is validating FSTs, the second step is mapping FSTs to genome. A user can upload the FASTA format, FASTQ format or PHD format FSTs. SeqIO module in BioPyhton is used for making the FASTA format file from the PHD format file. In addition, the user can upload the border sequences (ex, left or right border region from T-DNA), the adaptor sequence from adaptor-ligation PCR methods, and the binary vector sequence. And ‘minimum sequence length (MSL)’ is also chosen for FSTs validation; default MSL is 30bp. BLASTN analysis is used for masking vector sequence and finding position of the border and adaptor with expectation value of 10.0, 10.0, and 1e-10, respectively.

Binary vector and T-DNA tandem repeats were identified by sequence homology and it is indicated as a “vector”. Low quality sequences and sequences shorter than 'MSL' are indicated as a “Low (low quality sequence)” and a “NA (not acceptable sequence)”, respectively. The FSTs longer than 'MSL' are indicated as a “A (acceptable sequence)”. The acceptable FSTs are matched to genome using BLASTN with expected values of 5e-4. The highest scoring region is selected as an integration site of a the FST. This FSTs are divided into two types, genic region and intergenic region.

The FSTVAL provides the analysis result as a table. Additionally, masked sequences can be downloaded which are denoted as capital and lower-case according to a genomic sequence and a T-DNA border or an adaptor sequence, respectively. Then, the BLAST result is also presented as a table which shows the insertional type such as genic (exon, intron, 5’upstream-1000, 3’downstream-300), or intergenic. If the insertions occurred in a genic region, the interrupted gene id (which is linked to the GBrowser at its web site) and its description are shown. Also, if the FST is matched into intergenic region, the nearest gene from the insertion position is provided. We further established the distridution map and frequency graph of the insertions along the chromosomes using Python Image Library (PIL) and Matplotlib. The FSTVAL also provide 0.1-2kb regions sequence extending 5’ and 3’ from insertion position (that is indicated as five starts).

Scientific name	Common name	Source	Version	Reference
Arabidopsis lyrata	Lyrate rockcress	JGI	JGI release v1.0	Hu TT et al. (2011)
Arabidopsis thaliana	Aradidopsis	TAIR	TAIR10.0	Swarbreck D et al. (2008)
Brachypodium distachyon	Purple false brome	JGI	JGI v1.0 8x assembly, MIPS/JGI v1.0 annotation	International Brachypodium Initiative (2010)
Carica papaya	Papaya	ASGPB	December 2007	Ming R et al. (2008)
Chlamydomonas reinhardtii	Green algae	JGI	v4.3 release	Merchant SS et al. (2007)
Cucumis sativus	Cucumber	JGI	Phytozome v7.0	Huang S et al. (2009)
Glycine max	Soybean	JGI	Glyma1 release	Schmutz J et al. (2010)
Oryza sativa	Rice	MSU	MSU release 6.1	Ouyang S et al. (2007)
		RAP-DB	IRGSP/RAP build 5	Rice Annotation Project et al. (2007)
Physcomitrella patens	Moss	JGI	version 1.6	Rensing SA et al. (2008)
Populus trichocarpa	Western poplar	JGI	version 2.0	Tuskan GA et al. (2006)
Ricinus communis	Castor bean plant	JCVI	TIGR/JCVI release v0.1	Chan AP et al. (2010)
Sorghum bicolor	Cereal grass	JGI	v1.0 release (Sbi1 assembly, Sbi1.4 gene set)	Paterson AH et al. (2009)
Theobroma cacao	Cacao	USDA-ARS	Release 1.0	Argout X et al. (2011)
Vitis vinifera	Grape vine	Genoscope	March 2010 release	Jailon O et al. (2007)
Volvox carteri	Volvox	JGI	Phytozome v7.0	Prochnik SE et al. (2010)
Zea mays	Maize	Maizesequence	Release 5a	Schnable PS et al. (2009)
Brassica rapa	Chinese cabbage	BRAD	Release v1.1	Cheng F et al. (2011)

FSTVAL is:
Copyright (c) 2010-2012, MyongJi Univ. (or GreenGene BioTech Inc.), All rights reserved.
This source code is distributed under the terms of the GNU General Public License.
If you want to FSTVAL source code, send email to llmon7711@gmail.com.