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2019 | OriginalPaper | Chapter

An Overview of Multiple Sequence Alignment Methods Applied to Transmembrane Proteins

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

Published in: Technology Trends

Publisher: Springer International Publishing

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Abstract

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\(^\mathrm{TM}\), TM-Coffee and TM-Aligner. These methods have illustrated impressive advances in the accuracy and computational efforts aligning TMPs sequences.

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Title: An Overview of Multiple Sequence Alignment Methods Applied to Transmembrane Proteins
Authors: Cristian Zambrano-Vega
Byron Oviedo
Ronald Villamar-Torres
Miguel Botto-Tobar
Marcos Barros-Rodríguez
Publisher: Springer International Publishing
Book: Technology Trends
Print ISBN: 978-3-030-05531-8

Electronic ISBN: 978-3-030-05532-5

Copyright Year: 2019
DOI: https://doi.org/10.1007/978-3-030-05532-5_30

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