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Bioinformatics. 2015 May 15;31(10):1671-3. doi: 10.1093/bioinformatics/btv004. Epub 2015 Jan 11.

PASPA: a web server for mRNA poly(A) site predictions in plants and algae.

Author information

1
Department of Automation, Innovation Center for Cell Biology and Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, Department of Biology, Miami University, Oxford, OH, USA and Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China Department of Automation, Innovation Center for Cell Biology and Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, Department of Biology, Miami University, Oxford, OH, USA and Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
2
Department of Automation, Innovation Center for Cell Biology and Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, Department of Biology, Miami University, Oxford, OH, USA and Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
3
Department of Automation, Innovation Center for Cell Biology and Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, Department of Biology, Miami University, Oxford, OH, USA and Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China Department of Automation, Innovation Center for Cell Biology and Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, Department of Biology, Miami University, Oxford, OH, USA and Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China Department of Automation, Innovation Center for Cell Biology and Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, Department of Biology, Miami University, Oxford, OH, USA and Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.

Abstract

Polyadenylation is an essential process during 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 limited knowledge of poly(A) signals, it is still challenging to predict poly(A) sites in plants and algae. PASPA is a web server for P: oly( A: ) S: ite prediction in P: lants and A: lgae, which integrates many in-house tools as add-ons to facilitate poly(A) site prediction, visualization and mining. This server can predict poly(A) sites for ten species, including seven previously poly(A) signal non-characterized species, with sensitivity and specificity in a range between 0.80 and 0.95.

PMID:
25583118
DOI:
10.1093/bioinformatics/btv004
[Indexed for MEDLINE]

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