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2 results on '"Wohlers I"'

1. Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric

Author

Andonov, R. (Rumen), Djidjev, H. (Hristo), Klau, G.W. (Gunnar), Le Boudic-Jamin, M. (Mathilde), Wohlers, I. (Inken), Andonov, R. (Rumen), Djidjev, H. (Hristo), Klau, G.W. (Gunnar), Le Boudic-Jamin, M. (Mathilde), and Wohlers, I. (Inken)

Abstract

In this work, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all properties of a metric on the space of protein representations. Having a metric in that space allows one to avoid pairwise comparisons on the entire database and, thus, to significantly accelerate exploring the protein space compared to no-metric spaces. We show on a gold standard superfamily classification benchmark set of 6759 proteins that our exact k-nearest neighbor (k-NN) scheme classifies up to 224 out of 236 queries correctly and on a larger, extended version of the benchmark with 60; 850 additional structures, up to 1361 out of 1369 queries. Our k-NN classification thus provides a promising approach for the automatic classification of protein structures based on flexible contact map overlap alignments.

Published
2015
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2. Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing.

Author

Lüth T, Laβ J, Schaake S, Wohlers I, Pozojevic J, Jamora RDG, Rosales RL, Brüggemann N, Saranza G, Diesta CCE, Schlüter K, Tse R, Reyes CJ, Brand M, Busch H, Klein C, Westenberger A, and Trinh J

Subjects
Adult, Alu Elements, Humans, Male, Middle Aged, Minisatellite Repeats, Short Interspersed Nucleotide Elements, DNA Methylation, Dystonic Disorders genetics, Dystonic Disorders pathology, Epigenesis, Genetic, Genetic Diseases, X-Linked genetics, Genetic Diseases, X-Linked pathology, Nanopore Sequencing methods, Retroelements, TATA-Binding Protein Associated Factors genetics
Abstract

Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic ( CCCTCT ) n domain that acts as a genetic modifier of disease onset and expressivity., Methods: Herein, we used Nanopore sequencing to investigate SVA genetic variability and methylation. We used blood-derived DNA from 96 XDP patients for amplicon-based deep Nanopore sequencing and validated it with fragment analysis which was performed using fluorescence-based PCR. To detect methylation from blood- and brain-derived DNA, we used a Cas9-targeted approach., Results: High concordance was observed for hexanucleotide repeat numbers detected with Nanopore sequencing and fragment analysis. Within the SVA locus, there was no difference in genetic variability other than variations of the repeat motif between patients. We detected high CpG methylation frequency (MF) of the SVA and flanking regions (mean MF = 0.94, SD = ±0.12). Our preliminary results suggest only subtle differences between the XDP patient and the control in predicted enhancer sites directly flanking the SVA locus., Conclusions: Nanopore sequencing can reliably detect SVA hexanucleotide repeat numbers, methylation and, lastly, variation in the repeat motif.

Published
2022
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