Latent Periodicity of Protein Sequences

Korotkova, Maria A.; Korotkov, Eugene V.; Rudenko, V. М.

doi:10.1007/s008940050122

Cited by 29 publications

(24 citation statements)

References 3 publications

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“…All of these have detected a range of periodicities in a wide variety of data sets. Korotkova et al (Korotkova et al 1999) estimated that 10% of proteins in SwissProt were periodic, matching the figure of White & Jacobs (White and Jacobs 1993).…”

supporting

confidence: 52%

“…Since periodic sequences are non-random in composition, a Run Test might be expected to identify them (as well as identifying other types of non-random sequence), and this may therefore be taken as some evidence against widespread periodicity. Recently, with the availability of much larger sets of predicted protein sequences, a variety of approaches have been used, notably informational entropy (Korotkova et al 1999), and oligopeptide word frequencies (Katti et al 2000). All of these have detected a range of periodicities in a wide variety of data sets.…”

mentioning

confidence: 99%

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Phylogenetic Differences in Content and Intensity of Periodic Proteins

Gatherer

McEwan²

2005

J Mol Evol

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(247 words): Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-square-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 species reveals striking differences in the proportion of periodic proteins and the intensity of the most significant periodicities. Eukaryotes tend to have a higher proportion of periodic proteins than eubacteria, which in turn tend to have more than archaea. The intensity of periodicity in the most periodic proteins is also greatest in eukaryotes. By contrast, the relatively small group of periodic proteins in archaea also tend to be weakly periodic compared to those of eukaryotes and eubacteria. Exceptions to this general rule are found in those prokaryotes with multicellular life-cycle phases, e.g. Methanosarcina sps. or Anabaena sps., which have more periodicities than prokaryotes in general, and in unicellular eukaryotes, which have fewer than multicellular eukaryotes. The distribution of significantly periodic proteins in eukaryotes is over a wide range of period lengths, whereas prokaryotic proteins typically have a more limited set of period lengths. This is further investigated by repeating the analysis on the NRL-3D database of proteins of solved structure. Some short range periodicities are explicable in terms of basic secondary structure, e.g. alpha helices, while middle range periodicities are frequently found to consist of known short Pfam domains, e.g. leucine-rich repeats, tetratricopeptides or armadillo domains. However, not all can be explained in this way.3 Introduction:

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supporting

confidence: 52%

mentioning

confidence: 99%

Phylogenetic Differences in Content and Intensity of Periodic Proteins

Gatherer

McEwan²

2005

J Mol Evol

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“…It is generally accepted that protein molecules often have repetitive amino acid sequences of regular or latent (cryptic) periodicity [8][9][10][11]. The study of protein sequence periodicity is one of many approaches to find structural peculiarities of amino acid sequences and their relations with the spatial organization and function of proteins [10].…”

Section: Introductionmentioning

confidence: 99%

Distinctive amino acid residue periodicities in terminal sequences of type III and type I secreted proteins from proteobacteria

Andersone

Zikmanis

2007

Open Life Sciences

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Abstract:The Fourier transform (FT) method was applied to specify the distribution of 14 predefined groups of amino acids (64 residues) at both termini of annotated type III and type I secreted proteins from proteobacteria. Type I proteins displayed a higher occurrence of significant periodicities at both C-and N-termini, indicating potent features to discriminate between secretion types, particularly by the use of variables selected from the full periodicity profiles at 19 orders of FT. The Fishers linear discriminant analysis, together with the stepwise selection of variables throughout equal pairs of combinations for all predefined groups of residues, revealed the C-terminal harmonics of aromatic (HFWY) and aliphatic (VLIA) residues as a set of strong predictor variables to classify both types of secreted proteins with an accuracy of 100% for original grouped cases and 96.4% for cross-validated grouped cases. The prediction accuracy of proposed discriminant function was estimated by repeated kfold cross-validation procedures where the original data set was randomly divided into k subsets, with one of the k-subsets serving as the test set and the remaining data forming the training set. The average error rate computed across all k-trials and repeats did not exceed that of leave-one-out procedure. The proposed set of predictor variables could be used to assess the compatibility between secretion pathways and secretion substrates of proteobacteria by means of discriminant analysis.

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“…Для выявления периодичности в биологических строках ранее широко использовались методы Фурье-и вейвлет-анализа [17][18][19][20][21], комбинаторные методы и методы динамического программирования [1, 3,4,[22][23][24], различные статистические критерии проверки однородности строк [25][26][27][28][29] и др., см., например, обзор [30]. Однако по сравнению со статистическими критериями Фурье-анализ имеет плохую чувствительность к паттернам периодичности, размер которых в несколько раз превышает размер алфавита анализируемой строки [26].…”

Section: Introductionunclassified

“…Ранее предпринимались попытки создания эмпирических нестандартных критериев проверки однородности строк [26,27,29,33]. Строго говоря, эти критерии требуют для метода Монте-Карло генерации громадного числа перестановок ( 120 10 и более), так как не опираются на какую-либо теоретическую модель статистических экспериментов.…”

Section: Introductionunclassified

Joint Use of Different Homogeneity Testing Criteria for Latent Periodicity Revelation in Biological Sequences

Чалей¹,

Chaley²

2007

Math.Biol.Bioinf.

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Latent Periodicity of Protein Sequences

Cited by 29 publications

References 3 publications

Phylogenetic Differences in Content and Intensity of Periodic Proteins

Phylogenetic Differences in Content and Intensity of Periodic Proteins

Distinctive amino acid residue periodicities in terminal sequences of type III and type I secreted proteins from proteobacteria

Joint Use of Different Homogeneity Testing Criteria for Latent Periodicity Revelation in Biological Sequences

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