On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences

All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein...

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Detalles Bibliográficos
Autores principales:	Turjanski, P., Ferreiro, D.U.
Formato:	JOUR
Materias:	Amino acids Bioinformatics Structure (composition) Adjustable parameters Amino acid patterns Natural architecture Natural structures Precise definition Protein sequences Sequence patterns Standard deviation Proteins
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11295_Turjanski
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_15206106_v122_n49_p11295_Turjanski
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spelling	todo:paper_15206106_v122_n49_p11295_Turjanski2023-10-03T16:20:32Z On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences Turjanski, P. Ferreiro, D.U. Amino acids Bioinformatics Structure (composition) Adjustable parameters Amino acid patterns Natural architecture Natural structures Precise definition Protein sequences Sequence patterns Standard deviation Proteins All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for "repetition", an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust "familiarity" definition between arbitrary sets of sequences. © 2018 American Chemical Society. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11295_Turjanski
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Amino acids Bioinformatics Structure (composition) Adjustable parameters Amino acid patterns Natural architecture Natural structures Precise definition Protein sequences Sequence patterns Standard deviation Proteins
spellingShingle	Amino acids Bioinformatics Structure (composition) Adjustable parameters Amino acid patterns Natural architecture Natural structures Precise definition Protein sequences Sequence patterns Standard deviation Proteins Turjanski, P. Ferreiro, D.U. On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
topic_facet	Amino acids Bioinformatics Structure (composition) Adjustable parameters Amino acid patterns Natural architecture Natural structures Precise definition Protein sequences Sequence patterns Standard deviation Proteins
description	All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for "repetition", an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust "familiarity" definition between arbitrary sets of sequences. © 2018 American Chemical Society.
format	JOUR
author	Turjanski, P. Ferreiro, D.U.
author_facet	Turjanski, P. Ferreiro, D.U.
author_sort	Turjanski, P.
title	On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
title_short	On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
title_full	On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
title_fullStr	On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
title_full_unstemmed	On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
title_sort	on the natural structure of amino acid patterns in families of protein sequences
url	http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11295_Turjanski
work_keys_str_mv	AT turjanskip onthenaturalstructureofaminoacidpatternsinfamiliesofproteinsequences AT ferreirodu onthenaturalstructureofaminoacidpatternsinfamiliesofproteinsequences
_version_	1782026317394345984

On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences

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