Search Options available in piRNAQuest

Users can search for piRNAs by either entering piRNA ID or by entering chromosomal coordinates. The output will fetch detailed results of piRNAs.
Users can search for piRNAs in genes by either entering Gene Symbol or Gene Description or GO Term or Chromosomal Coordinates. The output table gives the detailed information of the genes and their corresponding piRNAs . Users can also search for piRNAs in Peudogenes by chromosomal coordinate.
piRNAs in a specific genomic location can be searched in repeats by using repeat family or repeat name. The results will give detailed information regarding piRNAs in the corresponding repeat family or repeat name.
piRNA clusters can be searched by users by entering chromosomal coordinate. One can also search for piRNA clusters present in genes and repeats as well. The output table will fetch detailed results of the piRNAs in repeat elements.
Users can search for syntenic piRNA clusters by chromosomal coordinates. The output table will fetch the piRNA clusters corresponding to syntenic regions.

Output formats of different search options

On searching by piRNAs the ouput will provide the genomic location of the piRNAs as well as their classification in gene, exon, intron, cds, 3'UTR, 5'UTR, repeat. Searching with chromosomal coordinates will retrieve piRNA loci, sequence, length.
The ouput for piRNAs contained in genes will retrieve the piRNAs corresponding to genes, the gene loci and the type of overlap with the gene. On searching with gene description one can check the genes of interest and then search for the piRNAs present in these genes.
The table on searching for piRNAs in repeat will retrieve piRNA loci, repeat loci, repeat name, repeat family and the type of overlap with repeat.
The output for piRNA clusters will contain the different cluster loci, cluster length, total piRNA present within the cluster, the % GC content and the type of motif present in the cluster. Moreover, a link to MEME has been provided to analyze the cluster motifs further.On searching genes overlapping with piRNA clusters will retrieve cluster loci, gene loci and the promoters corresponding to selected genes.
Searching for the syntenic piRNAs will retrieve the syntenic regions of target and query organism as well as the piRNA clusters present in this syntenic regions.A score has been provided which was obtained from blastz alignment from UCSC table browser.