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PRALINE: A Versatile Multiple Sequence Alignment Toolkit

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Multiple Sequence Alignment Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1079))

Abstract

Profile ALIgNmEnt (PRALINE) is a versatile multiple sequence alignment toolkit. In its main alignment protocol, PRALINE follows the global progressive alignment algorithm. It provides various alignment optimization strategies to address the different situations that call for protein multiple sequence alignment: global profile preprocessing, homology-extended alignment, secondary structure-guided alignment, and transmembrane aware alignment. A number of combinations of these strategies are enabled as well.

PRALINE is accessible via the online server http://www.ibi.vu.nl/programs/PRALINEwww/. The server facilitates extensive visualization possibilities aiding the interpretation of alignments generated, which can be written out in pdf format for publication purposes. PRALINE also allows the sequences in the alignment to be represented in a dendrogram to show their mutual relationships according to the alignment. The chapter ends with a discussion of various issues occurring in multiple sequence alignment.

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Notes

  1. 1.

    PRALINE finds the PDB identifier of a protein by extracting it from the fasta definition line of that protein. For example, these description lines are fine: “>102L_A,” “>102L|A,” and “>102LA”. For any other description line, PDB identifier is not extracted. No description may follow the sequence identifier. Thus “>pdb|102L|A”, “>gi|157829524|pdb|102L|A”, and also “>102L_A ” (note the trailing space) are skipped.

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Author information

Authors and Affiliations

  1. Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands

    Punto Bawono

  2. Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands

    Punto Bawono & Jaap Heringa

  3. Centre for Integrative Bioinformatics (IBIVU), Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands

    Jaap Heringa

Authors
  1. Punto Bawono
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  2. Jaap Heringa
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Editor information

Editors and Affiliations

  1. Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA

    David J Russell

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Bawono, P., Heringa, J. (2014). PRALINE: A Versatile Multiple Sequence Alignment Toolkit. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7_16

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  • DOI: https://doi.org/10.1007/978-1-62703-646-7_16

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-645-0

  • Online ISBN: 978-1-62703-646-7

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