TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner

Delucchi, Matteo; Näf, Paulina; Bliven, Spencer; Anisimova, Maria

doi:10.3389/fbinf.2021.691865

Cited by 14 publications

(10 citation statements)

References 43 publications

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“…To improve the accuracy and power of TR annotation, it has been suggested to apply a statistical framework in combination with a meta-approach that utilizes multiple TR prediction methods (Anisimova et al, 2015). We used Tandem Repeat Annotation Library (TRAL), which allows for evolutionary and statistics analyses to validate our annotated TRs (Schaper et al, 2015; Delucchi et al, 2021). Since MPXV genomes during 2022 outbreak most likely has a single origin (Isidro, et al, 2022), TRs in this study can be defined as related by a common ancestral unit under a Markov substitution model and a standard phylogeny model that reflects the unit duplication history (Schaper et al, 2012).…”

Section: Resultsmentioning

confidence: 99%

“…We used Tandem Repeat Annotation Library (TRAL 2.0), an open source Python 3 algorithm, to identify TR seed motifs from sequence profile databases via seven de novo TR algorithms (HHrepID, TRED, T-REKS, TRUST, XSTREAM, PHOBOS, TRF) (Schaper et al, 2015; Delucchi et al, 2021). Briefly, circular profile hidden Markov models (cpHMMs) were built from these TR seeds and then utilized to annotate TR regions in MPXV sequences.…”

Section: Methodsmentioning

confidence: 99%

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Recombination shapes 2022 monkeypox outbreak

Yeh

Hsieh

Feehley

et al. 2022

Preprint

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Here we report the first evidence of recombination of monkeypox genome in natural transmission by analyzing six tandem repeats (TRs) among 415 sequences collected between January to July 2022. The 2022 monkeypox viral population has diverged into 11 subgroups based on various TRs and their copy numbers. Here we identify 8 new recombinants (six from Slovenia, one from Australia, one from Italy). Our results indicate that the monkeypox genome is evolving and expanding quickly during the 2022 pandemic (Zeng E = -1.65, Achaz Y=-2.52, p< 0.001). We conclude that, In combination with genomic surveillance, TR analysis is a useful tool to monitor and track phylogenetic dynamics of monkeypox transmission.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Recombination shapes 2022 monkeypox outbreak

Yeh

Hsieh

Feehley

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Many algorithms have been used to detect tandem repeats (TRs) in biological sequences, leading to inconsistent TR annotations of identical sequences (Schaper et al 2012). To address this issue, we used the TRAL Python library (Delucchi et al 2021) which compares, harmonizes, and makes non-redundant, the output of different repeat detection algorithms (TRF, XSTREAM, PHOBOS, and T-REKS; see Methods). We used TRAL to annotate all SLC6A3 sequences for repeats.…”

Section: Resultsmentioning

confidence: 99%

“…In the present work, we used 64 publicly available long-read haplotype-phased genome assemblies from 32 individuals from the Human Genome Structural Variation Consortium (HGSVC) (Ebert et al 2021) and the Tandem Repeat Annotation Library (TRAL) Python library (Delucchi et al 2021) to characterize the VNTR landscape of SLC6A3 . We report the discovery of a novel hyper-variable number tandem repeat (hyVNTR) in the intron 8 region of SLC6A3 that has a consensus sequence length of 38 bp and repeat copy numbers ranging from 3.4-133.4.…”

Section: Introductionmentioning

confidence: 99%

A Novel Hyper-Variable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3)

Apsley

Domico

Verbiest

et al. 2022

Preprint

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The dopamine transporter gene, SLC6A3, has received substantial attention in genetic association studies of various phenotypes (hypertension, ADHD, substance use disorders, etc.). Although some variable number tandem repeats (VNTRs) present in SLC6A3 have been used as genetic markers in these association studies, results have not been consistent. We searched for unanalyzed VNTRs in SLC6A3 that might account for the heterogeneity of existing association study results. We used the Tandem Repeat Annotation Library (TRAL) to characterize the VNTR landscape of 64 unrelated long-read haplotype-phased SLC6A3 sequences. We further report sequence similarity of each repeat unit of the five VNTRs along with the correlations of SNP-SNP, SNP-VNTR and VNTR-VNTR alleles across the length of the gene. We present the discovery of a novel hyper-variable number tandem repeat (hyVNTR) in intron 8 of SLC6A3, which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38bp, with 84% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. Additionally, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it is a recombination hotspot.

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“…In the present work, we used 64 publicly available long-read haplotype-phased genome assemblies from 32 individuals from the Human Genome Structural Variation Consortium ( Ebert et al, 2021 ) and the Tandem Repeat Annotation Library (TRAL) Python library ( Delucchi et al, 2021 ) to characterize the VNTR landscape of SLC6A3 . We report the discovery of a novel hypervariable number tandem repeat (hyVNTR) in the intron 8 region of SLC6A3 that has a consensus sequence length of 38 bp and repeat copy numbers ranging from 3.4 to 133.4.…”

Section: Introductionmentioning

confidence: 99%

A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)

et al. 2023

Self Cite

View full text Add to dashboard Cite

The dopamine transporter gene,SLC6A3, has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats (VNTRs) present inSLC6A3have been tested in genetic association studies, results have not been consistent. VNTRs inSLC6A3that have not been examined genetically were characterized. The Tandem Repeat Annotation Library was used to characterize the VNTRs of 64 unrelated long-read haplotype-phasedSLC6A3sequences. Sequence similarity of each repeat unit of the five VNTRs is reported, along with the correlations of SNP–SNP, SNP–VNTR, and VNTR–VNTR alleles across the gene. One of these VNTRs is a novel hyper-VNTR (hyVNTR) in intron 8 ofSLC6A3, which contains a range of 3.4–133.4 repeat copies and has a consensus sequence length of 38 bp, with 82% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. In addition, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it might be a recombination hotspot.

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TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner

Cited by 14 publications

References 43 publications

Recombination shapes 2022 monkeypox outbreak

Recombination shapes 2022 monkeypox outbreak

A Novel Hyper-Variable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3)

A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)

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