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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2018
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v122_n49_p11295_Turjanski http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11295_Turjanski |
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paper:paper_15206106_v122_n49_p11295_Turjanski2025-07-30T18:54:54Z On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences 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. 2018 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v122_n49_p11295_Turjanski 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 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. |
| 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 |
| publishDate |
2018 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v122_n49_p11295_Turjanski http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11295_Turjanski |
| _version_ |
1840323299095085056 |