An overview of multiple sequence alignment methods applied to transmembrane proteins

Cristian Zambrano-Vega, Byron Oviedo, Ronald Villamar-Torres, Miguel Botto-Tobar, Marcos Barros-Rodríguez

    Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review


    Transmembrane proteins (TMPs) have received a great deal of attention playing a fundamental role in cell biology and are considered to constitute around 30% of proteins at genomic scale. Multiple Sequence Alignment (MSA) problem has been studied for some years and researchers have proposed many heuristic and stochastic techniques tailored for sequences of soluble proteins, considering that there are a few particular differences that ought to be taken into consideration aligning TMPs sequences, these techniques are therefore not optimal to align this special class of proteins. There is a small number of MSA methods applied specifically to TMPs. In this review, we have summarized the features, implementations and performance results of three MSA methods applied to TMPs: PRALINE™, ™-Coffee and TM-Aligner. These methods have illustrated impressive advances in the accuracy and computational efforts aligning TMPs sequences.

    Original languageEnglish
    Title of host publicationTechnology Trends - 4th International Conference, CITT 2018, Revised Selected Papers
    EditorsMiguel Botto-Tobar, Mayra D’Armas, Miguel Zúñiga Sánchez, Miguel Zúñiga-Prieto, Guillermo Pizarro
    Place of PublicationCham
    Number of pages10
    ISBN (Print)978-3-030-05531-8
    Publication statusPublished - 1 Jan 2019
    Event4th International Conference on Technology Trends, CITT 2018 - Babahoyo, Ecuador
    Duration: 29 Aug 201831 Aug 2018
    Conference number: 4

    Publication series

    NameCommunications in Computer and Information Science
    ISSN (Print)1865-0929


    Conference4th International Conference on Technology Trends, CITT 2018
    Abbreviated titleCITT 2018
    Internet address


    • Computational bilogy
    • Multiple sequence alignment
    • Transmembrane proteins
    • Multiple Sequence Alignment


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