Users can select a species and typing a genomic region such as chr1:1-2000000:+, gene symbol or Ensembl ID to query PAS cluster. Details of cluster with gene symbol, Ensembl ID, site ID, species, 3'UTR [extracted from DaPars2], PAS cluster, PAS clusterS, PAS, sampleP, sampleS and signals will be displayed in the table. Users can click the "Download" button to download the queried data, or click the "?" button for more information.

Users can select species and motif location (contain PAS hexamer, upstream 200 nt, downstream 200 nt) to query APA motif. A table with species, motif location, motif, countP and E-value will be returned. By clicking the “More Detail” button, Users can get reports from MEME or DREMW tool.

DaPars2 is based on detecting read density fluctuations in RNA-seq data
DaPars2 is the next generation of DaPars that directly infers the dynamic alternative polyadenylation (APA) usage by comparing standard RNA-seq from multiple samples. Given the annotated gene model, DaPars2 can infer the de novo proximal APA sites as well as the long and short 3'UTR expression levels. Finally, the dynamic APA usages of each samples will be identified.

QAPA relies on priori annotations of poly(A) sites
QAPA (quantification of APA) employs an expanded library of annotated poly(A) sites to refine 3'UTRs and quantify relative abundance of APA isoforms. It first curates a library of 3'UTR isoform sequences by refining existing 3′ UTRs or adding new 3′ UTRs based on additional poly(A) site annotation sources. These new 3'UTR sequences are then used to measure transcript-level expression of 3'UTRs using a pseudo-alignment tool called Sailfish, which is the main difference between QAPA and many other methods. Then the relative usage of a 3'UTR isoform (called PAU, Poly(A) Usage) was calculated as the normalized expression of a 3′ UTR over the total expression level of all 3'UTRs in a gene. The change of APA site usage is measured by the PAU of the proximal poly(A) site.

Note
Required files used in DaPars2 and QAPA process can be obtained through the steps suggested by the official documents (QAPA and DaPars / DaPars2). And it was very important that 3'UTR annotation region in this website was extracted from DaPars2.

The annotation of last exons were collected from the UCSC and Ensembl. Two different algorithms were used to calculated APA events for each gene in each tissue from different species. For DaPars2, we calculated the percentage of distal poly(A) site usage index (PDUI) of APA events, and required that the average normalized reads of each 3'UTR region is ≥ 30. And at the same time, we deleted the sites which the SampleP was < 5%. For QAPA, it can calculate the poly(A) usage (PAU) by ploy(A) site annotation files from GENCODE basic poly(A) annotation track, PolyASite or custom file. We filtered sites which sampleP was < 5% and add PolyASite's annotation file which sampleP was ≥ 5% for mouse and worm.