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

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™, ™-Coffee and TM-Aligner. These methods have illustrated impressive advances in the accuracy and computational efforts aligning TMPs sequences.

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
PublisherSpringer
Pages410-419
Number of pages10
ISBN (Print)978-3-030-05531-8
DOIs
StatePublished - 1 Jan 2019
Event4th International Conference on Technology Trends, CITT 2018 - Babahoyo, Ecuador
Duration: 29 Aug 201831 Aug 2018
Conference number: 4
http://citt.utb.edu.ec

Publication series

NameCommunications in Computer and Information Science
Volume895
ISSN (Print)1865-0929

Conference

Conference4th International Conference on Technology Trends, CITT 2018
Abbreviated titleCITT 2018
CountryEcuador
CityBabahoyo
Period29/08/1831/08/18
Internet address

Fingerprint

Multiple Sequence Alignment
Proteins
Protein
Protein Sequence
Cytology
Coffee
Biology
Genomics
Heuristics
Cell

Keywords

  • Computational bilogy
  • Multiple sequence alignment
  • Transmembrane proteins

Cite this

Zambrano-Vega, C., Oviedo, B., Villamar-Torres, R., Botto-Tobar, M., & Barros-Rodríguez, M. (2019). An overview of multiple sequence alignment methods applied to transmembrane proteins. In M. Botto-Tobar, M. D’Armas, M. Zúñiga Sánchez, M. Zúñiga-Prieto, & G. Pizarro (Eds.), Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers (pp. 410-419). (Communications in Computer and Information Science; Vol. 895). Cham: Springer. DOI: 10.1007/978-3-030-05532-5_30
Zambrano-Vega, Cristian ; Oviedo, Byron ; Villamar-Torres, Ronald ; Botto-Tobar, Miguel ; Barros-Rodríguez, Marcos. / An overview of multiple sequence alignment methods applied to transmembrane proteins. Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. editor / Miguel Botto-Tobar ; Mayra D’Armas ; Miguel Zúñiga Sánchez ; Miguel Zúñiga-Prieto ; Guillermo Pizarro. Cham : Springer, 2019. pp. 410-419 (Communications in Computer and Information Science).
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title = "An overview of multiple sequence alignment methods applied to transmembrane proteins",
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™, ™-Coffee and TM-Aligner. These methods have illustrated impressive advances in the accuracy and computational efforts aligning TMPs sequences.",
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Zambrano-Vega, C, Oviedo, B, Villamar-Torres, R, Botto-Tobar, M & Barros-Rodríguez, M 2019, An overview of multiple sequence alignment methods applied to transmembrane proteins. in M Botto-Tobar, M D’Armas, M Zúñiga Sánchez, M Zúñiga-Prieto & G Pizarro (eds), Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. Communications in Computer and Information Science, vol. 895, Springer, Cham, pp. 410-419, 4th International Conference on Technology Trends, CITT 2018, Babahoyo, Ecuador, 29/08/18. DOI: 10.1007/978-3-030-05532-5_30

An overview of multiple sequence alignment methods applied to transmembrane proteins. / Zambrano-Vega, Cristian; Oviedo, Byron; Villamar-Torres, Ronald; Botto-Tobar, Miguel; Barros-Rodríguez, Marcos.

Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. ed. / Miguel Botto-Tobar; Mayra D’Armas; Miguel Zúñiga Sánchez; Miguel Zúñiga-Prieto; Guillermo Pizarro. Cham : Springer, 2019. p. 410-419 (Communications in Computer and Information Science; Vol. 895).

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

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Zambrano-Vega C, Oviedo B, Villamar-Torres R, Botto-Tobar M, Barros-Rodríguez M. An overview of multiple sequence alignment methods applied to transmembrane proteins. In Botto-Tobar M, D’Armas M, Zúñiga Sánchez M, Zúñiga-Prieto M, Pizarro G, editors, Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. Cham: Springer. 2019. p. 410-419. (Communications in Computer and Information Science). Available from, DOI: 10.1007/978-3-030-05532-5_30