title: Wheat Zapper: a flexible online tool for colinearity studies in grass genomes.
abstract: In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The "Wheat Zapper" application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the "Wheat Zapper" prediction was confirmed against the genome of maize, with good correlation (r > 0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of "Wheat Zapper" was calculated at 0.65 considering the "Genome Zipper" application as the "gold" standard. The differences between these two tools are amply discussed, making the point that "Wheat Zapper" is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/ .
authors.affiliation: Computer Information Systems Department, The University of Jordan, Amman, 11942, Jordan.
authors.forename: Loai M
authors.initials: LM
authors.lastname: Alnemer
authors.forename: Raed I
authors.initials: RI
authors.lastname: Seetan
authors.forename: Filippo M
authors.initials: FM
authors.lastname: Bassi
authors.forename: Charith
authors.initials: C
authors.lastname: Chitraranjan
authors.forename: Adam
authors.initials: A
authors.lastname: Helsene
authors.forename: Paul
authors.initials: P
authors.lastname: Loree
authors.forename: Steve Bou
authors.initials: SB
authors.lastname: Goshn
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.forename: M Javed
authors.initials: MJ
authors.lastname: Iqbal
authors.forename: Gerard R
authors.initials: GR
authors.lastname: Lazo
authors.forename: Anne M
authors.initials: AM
authors.lastname: Denton
authors.forename: Shahryar F
authors.initials: SF
authors.lastname: Kianian
mesh_terms: D018745:Genome, Plant; D006109:Poaceae / Q000235:genetics*; D012984:Software; D026801:Synteny