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repetitive elements in bioinformatics

Epub 2020 Aug 10.

2020 Aug;6(8):929-941. doi: 10.1038/s41477-020-0735-y. 2020 Jul 21;11:1484. doi: 10.3389/fmicb.2020.01484. In the original study described above (Fleischer et al., Importantly, analyses of RE in RNA‐seq data are inherently challenging and artifact‐prone because of the many RE copies and their various locations in the genome. Sequence comparisons in RepeatMasker are usually performed by the alignment program cross_match, which requires significant processing time for larger sequences. 2020 Aug 1;7:122. doi: 10.1038/s41438-020-00343-8. 2009;537:323-36. doi: 10.1007/978-1-59745-251-9_16.Bioinformatics. Epub 2005 Nov 15.Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J.Cytogenet Genome Res.

The two most common terms used for sequences containing short repeating units are simple sequence repeat (SSR) and microsatellite. Clipboard, Search History, and several other advanced features are temporarily unavailable. Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation.

Classic genomic markers like telomere length and the epigenetic clock have been useful for studying age and factors that accelerate aging in many settings. BMC Bioinformatics, 2006 Oct 25;7:474. Here, we used multiple RNA‐seq datasets generated from human samples and Older age is the primary risk factor for disability and chronic diseases, and as a result, there is significant interest in identifying mechanisms and markers of aging (Partridge, Deelen, & Slagboom, One particularly large and often‐ignored fraction of the human genome (>60%) is composed of repetitive elements (RE). Transcriptomic markers of aging can be useful for studying age‐related processes and diseases. Further, the advantages, limitations, and known bugs of the software are discussed. Although the elongation of SSR tracts may be due to more than one mechanism , much is thought to be the result of slip-strand replication errors. (d) Linear regression predicting actual age based on the top 1,200 genes most differentially expressed with aging. COVID-19 is an emerging, rapidly evolving situation.

Here, we describe two Basic Protocols that provide detailed guidelines on how to use RepeatMasker, either via the Web interface or command-line Unix/Linux system, to analyze repetitive elements in genomic sequences. eCollection 2020.Liu X, Li B, Yang Y, Cai J, Shi T, Zheng X, Huang G.Front Microbiol. TJL drafted the manuscript with input and assistance from all authors, and TJL, ANC, and DW edited the final manuscript.The data that support the findings of this study (RNA‐seq datasets) are available in the Gene Expression Omnibus (GEO), accession numbers Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. These include: types 1 and 2 transposons (retrotransposons and DNA transposons, respectively), some of which can self‐copy and reinsert into new locations; terminal repeats (at the ends of retrotransposons); and tandem repeats (including sequences common to centromeres, chromatin, and other structured genome regions) (Cordaux & Batzer, To determine whether RE transcripts increase globally with aging, we first examined a total RNA‐seq dataset generated from dermal fibroblasts of 133 healthy subjects aged 1–94 years (Fleischer et al., Could a global increase in RE transcripts be a good transcriptomic marker of age/aging? eCollection 2020.Wang J, Liu W, Zhu D, Hong P, Zhang S, Xiao S, Tan Y, Chen X, Xu L, Zong X, Zhang L, Wei H, Yuan X, Liu Q.Hortic Res. They have impact on both genome evolution and regulation. Curr Protoc Bioinformatics. 2020 Aug 3;11:1866. doi: 10.3389/fmicb.2020.01866.

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An Alternate Protocol describes how to reduce the processing time using an alternative alignment program, such as WU-BLAST.

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