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DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method

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Viral Metagenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1746))

Abstract

Multiple sequence alignment (MSA) is a fundamental component in many DNA sequence analyses including metagenomics studies and phylogeny inference. When guided by protein profiles, DNA multiple alignments assume a higher precision and robustness. Here we present details of the use of the upgraded version of MSA-PAD (2.0), which is a DNA multiple sequence alignment framework able to align DNA sequences coding for single/multiple protein domains guided by PFAM or user-defined annotations. MSA-PAD has two alignment strategies, called “Gene” and “Genome,” accounting for coding domains order and genomic rearrangements, respectively. Novel options were added to the present version, where the MSA can be guided by protein profiles provided by the user. This allows MSA-PAD 2.0 to run faster and to add custom protein profiles sometimes not present in PFAM database according to the user’s interest. MSA-PAD 2.0 is currently freely available as a Web application at https://recasgateway.cloud.ba.infn.it/.

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Acknowledgment

This work was supported by the Italian nodes of Lifewatch and ELIXIR Research Infrastructures.

Author information

Authors and Affiliations

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, Italy

    Bachir Balech, Monica Santamaria & Graziano Pesole

  2. National Institute of Nuclear Physics, Bari, Italy

    Alfonso Monaco, Michele Perniola, Giacinto Donvito & Giorgio Maggi

  3. Institute of Atmospheric Pollution Research, CNR, c/o Department of Physics, University of Bari “A. Moro”, Bari, Italy

    Saverio Vicario

  4. Politecnico di Bari, Bari, Italy

    Giorgio Maggi

  5. Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Bari, Italy

    Graziano Pesole

Authors
  1. Bachir Balech
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  2. Alfonso Monaco
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  3. Michele Perniola
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  4. Monica Santamaria
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  5. Giacinto Donvito
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  6. Saverio Vicario
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  7. Giorgio Maggi
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  8. Graziano Pesole
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Editor information

Editors and Affiliations

  1. Institute Sustainable Plant Protection of the CNR, Research Unit of Bari, Bari, Italy

    Vitantonio Pantaleo

  2. Institute Sustainable Plant Protection of the CNR, Research Unit of Bari, Bari, Italy

    Michela Chiumenti

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Balech, B. et al. (2018). DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method. In: Pantaleo, V., Chiumenti, M. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 1746. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7683-6_13

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  • DOI: https://doi.org/10.1007/978-1-4939-7683-6_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7682-9

  • Online ISBN: 978-1-4939-7683-6

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