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

doi:10.1007/978-3-030-05532-5_30

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

Onderzoeksoutput: Hoofdstuk in Boek/Rapport/Congresprocedure › Conferentiebijdrage › Academic › peer review

Samenvatting

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.

Originele taal-2	Engels
Titel	Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers
Redacteuren	Miguel Botto-Tobar, Mayra D’Armas, Miguel Zúñiga Sánchez, Miguel Zúñiga-Prieto, Guillermo Pizarro
Plaats van productie	Cham
Uitgeverij	Springer
Pagina's	410-419
Aantal pagina's	10
ISBN van geprinte versie	978-3-030-05531-8
DOI's	https://doi.org/10.1007/978-3-030-05532-5_30
Status	Gepubliceerd - 1 jan. 2019
Evenement	4th International Conference on Technology Trends, CITT 2018 - Babahoyo, Ecuador Duur: 29 aug. 2018 → 31 aug. 2018 Congresnummer: 4 http://citt.utb.edu.ec

Publicatie series

Naam	Communications in Computer and Information Science
Volume	895
ISSN van geprinte versie	1865-0929

Congres

Congres	4th International Conference on Technology Trends, CITT 2018
Verkorte titel	CITT 2018
Land/Regio	Ecuador
Stad	Babahoyo
Periode	29/08/18 → 31/08/18
Internet adres	http://citt.utb.edu.ec

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10.1007/978-3-030-05532-5_30

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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 (editors), Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers (blz. 410-419). (Communications in Computer and Information Science; Vol. 895). Springer. https://doi.org/10.1007/978-3-030-05532-5_30

Zambrano-Vega, Cristian ; Oviedo, Byron ; Villamar-Torres, Ronald et al. / An overview of multiple sequence alignment methods applied to transmembrane proteins. Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. redacteur / Miguel Botto-Tobar ; Mayra D’Armas ; Miguel Zúñiga Sánchez ; Miguel Zúñiga-Prieto ; Guillermo Pizarro. Cham : Springer, 2019. blz. 410-419 (Communications in Computer and Information Science).

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

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author = "Cristian Zambrano-Vega and Byron Oviedo and Ronald Villamar-Torres and Miguel Botto-Tobar and Marcos Barros-Rodr{\'i}guez",

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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 (uitgave), Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. Communications in Computer and Information Science, vol. 895, Springer, Cham, blz. 410-419, 4th International Conference on Technology Trends, CITT 2018, Babahoyo, Ecuador, 29/08/18. https://doi.org/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 et al.
Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. uitgave / Miguel Botto-Tobar; Mayra D’Armas; Miguel Zúñiga Sánchez; Miguel Zúñiga-Prieto; Guillermo Pizarro. Cham: Springer, 2019. blz. 410-419 (Communications in Computer and Information Science; Vol. 895).

Onderzoeksoutput: Hoofdstuk in Boek/Rapport/Congresprocedure › Conferentiebijdrage › Academic › peer review

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AU - Zambrano-Vega, Cristian

AU - Oviedo, Byron

AU - Villamar-Torres, Ronald

AU - Botto-Tobar, Miguel

AU - Barros-Rodríguez, Marcos

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N2 - 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.

AB - 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. 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, redacteurs, Technology Trends - 4th International Conference, CITT 2018, Revised Selected Papers. Cham: Springer. 2019. blz. 410-419. (Communications in Computer and Information Science). doi: 10.1007/978-3-030-05532-5_30

An overview of multiple sequence alignment methods applied to transmembrane proteins

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