PANDA: Protein function prediction using domain architecture and affinity propagation

Scientific Reports
Zheng WangNan Wang

Abstract

We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions in the format of Gene Ontology (GO) terms. PANDA at first executes profile-profile alignment algorithm to search against PfamA, KOG, COG, and SwissProt databases, and then launches PSI-BLAST against UniProt for homologue search. PANDA integrates a domain architecture inference algorithm based on the Bayesian statistics that calculates the probability of having a GO term. All the candidate GO terms are pooled and filtered based on Z-score. After that, the remaining GO terms are clustered using an affinity propagation algorithm based on the GO directed acyclic graph, followed by a second round of filtering on the clusters of GO terms. We benchmarked the performance of all the baseline predictors PANDA integrates and also for every pooling and filtering step of PANDA. It can be found that PANDA achieves better performances in terms of area under the curve for precision and recall compared to the baseline predictors. PANDA can be accessed from http://dna.cs.miami.edu/PANDA/ .

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Citations

Sep 17, 2019·Current Protocols in Bioinformatics·Archana S Bhat, Nick V Grishin
Jul 14, 2020·Bioinformatics·Moses StamboulianPredrag Radivojac
Nov 8, 2019·Computational Biology and Chemistry·Sarthak MishraShabnam Khatun
Mar 9, 2021·Computational and Structural Biotechnology Journal·Yan WangZhidong Xue
May 22, 2021·Nucleic Acids Research·Maxat KulmanovRobert Hoehndorf
Oct 21, 2021·PloS One·Pahalage Dhanushka Sandaruwan, Champi Thusangi Wannige

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Software Mentioned

PfamScan
TASSER
PSI
HHblits
multiPfamgo
GOGO
lite
fastSemSim
BLAST
GO

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