Gabriele Orlando1,2,3,4, Daniele Raimondi1,2,3,4, Taushif Khan1,2, Tom Lenaerts1,4,5, Wim F Vranken1,2,3. 1. Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan. 2. Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2. 3. Structural Biology Research Center, VIB. 4. Structural Machine Learning Group, Université Libre de Bruxelles. 5. Artificial Intelligence Lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
Abstract
MOTIVATION: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. RESULTS: Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. AVAILABILITY AND IMPLEMENTATION: A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. CONTACT: wim.vranken@vub.be. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. RESULTS: Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. AVAILABILITY AND IMPLEMENTATION: A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. CONTACT: wim.vranken@vub.be. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Luciano Kagami; Joel Roca-Martínez; Jose Gavaldá-García; Pathmanaban Ramasamy; K Anton Feenstra; Wim F Vranken Journal: BMC Mol Cell Biol Date: 2021-04-23