TwinCons: Conservation score for uncovering deep sequence similarity and divergence.

We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one group to the other at each position of t...

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Autores principales:	Petar I Penev, Claudia Alvarez-Carreño, Eric Smith, Anton S Petrov, Loren Dean Williams
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b8aec4db844f4ec1adda39cb98b36cd8
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spelling	oai:doaj.org-article:b8aec4db844f4ec1adda39cb98b36cd82021-12-02T19:57:40ZTwinCons: Conservation score for uncovering deep sequence similarity and divergence.1553-734X1553-735810.1371/journal.pcbi.1009541https://doaj.org/article/b8aec4db844f4ec1adda39cb98b36cd82021-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009541https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one group to the other at each position of the alignment. The output distinguishes conserved, variable and signature positions. A signature is conserved within groups but differs between groups. The method automatically detects continuous characteristic stretches (segments) within alignments. TwinCons provides a convenient representation of conserved, variable and signature positions as a single score, enabling the structural mapping and visualization of these characteristics. Structure is more conserved than sequence. TwinCons highlights alternative sequences of conserved structures. Using TwinCons, we detected highly similar segments between proteins from the translation and transcription systems. TwinCons detects conserved residues within regions of high functional importance for the ribosomal RNA (rRNA) and demonstrates that signatures are not confined to specific regions but are distributed across the rRNA structure. The ability to evaluate both nucleic acid and protein alignments allows TwinCons to be used in combined sequence and structural analysis of signatures and conservation in rRNA and in ribosomal proteins (rProteins). TwinCons detects a strong sequence conservation signal between bacterial and archaeal rProteins related by circular permutation. This conserved sequence is structurally colocalized with conserved rRNA, indicated by TwinCons scores of rRNA alignments of bacterial and archaeal groups. This combined analysis revealed deep co-evolution of rRNA and rProtein buried within the deepest branching points in the tree of life.Petar I PenevClaudia Alvarez-CarreñoEric SmithAnton S PetrovLoren Dean WilliamsPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 10, p e1009541 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Petar I Penev Claudia Alvarez-Carreño Eric Smith Anton S Petrov Loren Dean Williams TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
description	We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one group to the other at each position of the alignment. The output distinguishes conserved, variable and signature positions. A signature is conserved within groups but differs between groups. The method automatically detects continuous characteristic stretches (segments) within alignments. TwinCons provides a convenient representation of conserved, variable and signature positions as a single score, enabling the structural mapping and visualization of these characteristics. Structure is more conserved than sequence. TwinCons highlights alternative sequences of conserved structures. Using TwinCons, we detected highly similar segments between proteins from the translation and transcription systems. TwinCons detects conserved residues within regions of high functional importance for the ribosomal RNA (rRNA) and demonstrates that signatures are not confined to specific regions but are distributed across the rRNA structure. The ability to evaluate both nucleic acid and protein alignments allows TwinCons to be used in combined sequence and structural analysis of signatures and conservation in rRNA and in ribosomal proteins (rProteins). TwinCons detects a strong sequence conservation signal between bacterial and archaeal rProteins related by circular permutation. This conserved sequence is structurally colocalized with conserved rRNA, indicated by TwinCons scores of rRNA alignments of bacterial and archaeal groups. This combined analysis revealed deep co-evolution of rRNA and rProtein buried within the deepest branching points in the tree of life.
format	article
author	Petar I Penev Claudia Alvarez-Carreño Eric Smith Anton S Petrov Loren Dean Williams
author_facet	Petar I Penev Claudia Alvarez-Carreño Eric Smith Anton S Petrov Loren Dean Williams
author_sort	Petar I Penev
title	TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
title_short	TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
title_full	TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
title_fullStr	TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
title_full_unstemmed	TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
title_sort	twincons: conservation score for uncovering deep sequence similarity and divergence.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/b8aec4db844f4ec1adda39cb98b36cd8
work_keys_str_mv	AT petaripenev twinconsconservationscoreforuncoveringdeepsequencesimilarityanddivergence AT claudiaalvarezcarreno twinconsconservationscoreforuncoveringdeepsequencesimilarityanddivergence AT ericsmith twinconsconservationscoreforuncoveringdeepsequencesimilarityanddivergence AT antonspetrov twinconsconservationscoreforuncoveringdeepsequencesimilarityanddivergence AT lorendeanwilliams twinconsconservationscoreforuncoveringdeepsequencesimilarityanddivergence
_version_	1718375799033167872

TwinCons: Conservation score for uncovering deep sequence similarity and divergence.

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