PASPA: a web server for poly(A) site prediction in plants and algae

●  Motivation

Polyadenylation is a critical regulator for eukaryotic gene expression. Prediction of poly(A) sites helps to define the 3’ end of genes, which is important for gene annotation and elucidating gene regulation mechanisms. However, due to the limited knowledge of poly(A) signals, it is still challenging to predict poly(A) sites in plants and algae.

●  What is PASPA ?

PASPA is a web server for poly(A) site prediction in plants and algae. Currently, PASPA can predict poly(A) sites for ten species, including Arabidopsis, rice, and Medicago truncatula,spikemoss Selaginella moellendorffii, moss Physcomitrella patens, red algae Cyanidioschyzon merolae, two green algae C. reinhardtii and Ostreococcus lucimarinus, and two diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum.

●  Getting started

The input for PASPA are a DNA sequence file in FASTA format, with the optional files for known poly(A) sites. The output is the predicted poly(A) site(s) based on poly(A) scores. The result pages contain three viewers. (1) List viewer: showing predicted poly(A) sites, single nucleotide base compositions, and poly(A) signals of the input sequences. (2) Score viewer: showing score curve and poly(A) signal of a selected sequence. (3) EST-polyA viewer: showing genome alignment and known poly(A) sites of the selected sequence.

To start a task for poly(A) site prediction, click here. A task ID will be assigned for each task. You can retrieve the result of your task at our Data Retrival Page. You can also view all tasks you started at the Data Retrival Page. Click here for a step by step guide. You can browse a demo task here.

●  Availability

PASPA was developed by the bioinformatics group and biology group at Xiamen University and Miami University. The Download page links to software package, Perl scripts, model parameter files, and compiled data sets for PASPA.

Please cite the following paper when using the PASPA.

Ji G, Li L, Li QQ, Wu X, Fu J, Chen G, Wu X: PASPA: a web server for mRNA poly(A) site predictions in plants and algae. Bioinformatics 2015, 31(10):1671-1673.

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