What is Wheat Zapper!
      
Wheat Zapper is a fast and flexible on-line application to predict orthologus relationships between wheat genes and the fully sequenced model species Oryza sativa, Brachypodium dystachyon, and Sorghum bicolor. When synteny is conserved (i.e. the query sequences are orthologus to genes from the same chromosome), Zapper finds all the genes within the synteny interval and their corresponding wheat EST.
       Wheat Zapper is an ideal software for markers saturation of specific regions, such as in fine mapping projects, but it also adapts perfectly to genomic studies or evolutionary analysis. Wheat Zapper was originally developed for wheat studies, but the simplicity and flexibility of the algorithm can be readily applied to any species. 

Inputs and Outputs of Wheat Zapper!
       The input of Zapper is any sequences, minimum 2 and maximum 100, in FASTA format from any species. The output of Zapper can be immediately converted into Excel sheet, used as input for primer design software or for graphical representation of colinearity. Zapper also provides all the wheat ESTs sequences of an interval as output file, ready to be used for microarray design or predicting gene functions. Zapper implements also an intron/exon junction prediction algorithm based on cDNA/gDNA alignments that can be used as input for SNP or HSV primer design using the data available from survey sequencing projects.

How Wheat Zapper Works!
1- Input any partial or complete marker, EST or gene DNA sequences (min 2 max 100). Note: inter-gene space is not conserved across species, so genic sequences are more likely to find orthologus relationships.



2- Submit. It takes approximately 1 minute to find the orthologus genes for a three sequences search.

3- Select the two sequences underling the syntenic interval you are interested into. The software will automatically select for you (checked and yellow rows) the largest possible interval .



In the example above, the two EST suggested by the software ( in yellow) are used to find all the possible orthologus genes from rice, bracy and sorghum.

Special Case:
If the synteny is conserved only for part of the genes, then the user can only select the conserved interval.



In the example above, TC370753 does not underline a syntenic interval and hence can not be selected by the user.
If the synteny is not conserved (i.e. Zapper has analyzed all genes orthologus to the input query, at values below the selected E, and could not find two orthologus genes to underline a syntenic interval) then the user cannot select any of the genes.



In the example above, no syntenic interval was found and hence all the selection button are disabled

4- Submit and go take a long coffee, but do not forget to save the job ID (355 in the above example) to retrieve your results later. Zapper is retrieving all the genes within your selected interval from all the three sequenced species, searching them back against the full length wheat EST, and saving them for you in a nice user-friendly format. Note: the largest is the interval the longest it is going to take.

5- Zapper outputs a table to summarize all the orthologus relationships. The gene function is reported as indicated by the Rice Annotation Project database. Locus name and physical position are also reported. All orthologus genes are reported sorted based on rice, then brachy, and finally sorghum. The table can be downloaded as a text file that can be readily converted into an excel sheet clicking the ‘Get Table’ option.

6- The EST sequences can be downloaded using the ‘Download EST Sequences’ option

7- Intron/Exon junctions can be predicted for some or all of the EST using the ‘Find Exon/Intron’ command.





A graphic presentation is shown using  Circos 0.53 tool when you hit Pretty Picture button



8-  Two primers design softwares available on the website, when user press on Design Primers button. the size of the primers varies depending on the exists of Intron/Exon junctions, we indicate "+I"  to show primers design that span the junctions, on the primers that have Intron/Exon junctions.



Note:
Your job will be saved for 1 week. You can retrieve your job using retrieve job link.