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International Conference on Practical Applications of Computational Biology & Bioinformatics

PACBB2018 2018: Practical Applications of Computational Biology and Bioinformatics, 12th International Conference pp 149–156Cite as

EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species

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Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 803))

Abstract

Biological processes are mediated by protein-protein interactions (PPI) that have been studied using different methodologies, and organized as centralized repositories - PPI databases. The data stored in the different PPI databases only overlaps partially. Moreover, some of the repositories are dedicated to a species or subset of species, not all have the same functionalities, or store data in the same format, making comparisons between different databases difficult to perform. Therefore, here we present EvoPPI (http://evoppi.i3s.up.pt), an open source web application tool that allows users to compare the protein interactions reported in two different interactomes. When interactomes belong to different species, a versatile BLAST search approach is used to identify orthologous/paralogous genes, which to our knowledge is a unique feature of EvoPPI.

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Acknowledgements

Sara Rocha and this work are supported by the project Norte-01-0145-FEDER-000008 - Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068-0). SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure. Financial support from the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2016-2019) and the European Union (European Regional Development Fund - ERDF), is gratefully acknowledged.

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Authors and Affiliations

  1. ESEI - Escuela Superior de Ingeniería Informática, Universidad de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain

    Noé Vázquez, Hugo López-Fernández, Florentino Fdez-Riverola & Miguel Reboiro-Jato

  2. Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain

    Noé Vázquez, Hugo López-Fernández, Florentino Fdez-Riverola & Miguel Reboiro-Jato

  3. Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal

    Sara Rocha, Hugo López-Fernández, André Torres, Jorge Vieira & Cristina P. Vieira

  4. Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal

    Sara Rocha, Hugo López-Fernández, André Torres, Jorge Vieira & Cristina P. Vieira

  5. SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain

    Hugo López-Fernández, Florentino Fdez-Riverola & Miguel Reboiro-Jato

  6. LIAAD, DEI, Faculdade de Engenharia, Universidade do Porto, Porto, Portugal

    Rui Camacho

Authors
  1. Noé Vázquez
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  2. Sara Rocha
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  3. Hugo López-Fernández
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  4. André Torres
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  5. Rui Camacho
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  6. Florentino Fdez-Riverola
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  7. Jorge Vieira
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  8. Cristina P. Vieira
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  9. Miguel Reboiro-Jato
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Corresponding author

Correspondence to Hugo López-Fernández .

Editor information

Editors and Affiliations

  1. Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain

    Florentino Fdez-Riverola

  2. Faculty of Computing, Department of Software Engineering, Universiti Teknologi Malaysia, Johor, Malaysia

    Mohd Saberi Mohamad

  3. Department de Informática, Universidade do Minho, Braga, Portugal

    Miguel Rocha

  4. Departamento de Informática y Automática, Facultad de Ciencias, Universidad de Salamanca, Salamanca, Spain

    Juan F. De Paz

  5. Departamento de Sistemas Informáticos, Universidad de Castilla-La Mancha, Albacete, Albacete, Spain

    Pascual González

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Vázquez, N. et al. (2019). EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., González, P. (eds) Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. PACBB2018 2018. Advances in Intelligent Systems and Computing, vol 803. Springer, Cham. https://doi.org/10.1007/978-3-319-98702-6_18

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