Identifies repetitive sequences and reconstructs separated sections to provide full-length repeats and, for long-terminal repeat (LTR) retrotransposons, calculates age since insertion based on LTR divergence. TEnest is a repeat identification and display tool made specifically for highly repetitive genomes. It provides a chronological insertion display to give an accurate visual representation of transposable element (TE) integration history showing timeline, location, and families of each TE identified, thus creating a framework from which evolutionary comparisons can be made among various regions of the genome.
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A collection of software tools for characterization of repetitive elements, which is accessible via web interface. A key component of the server is the computational pipeline using a graph-based sequence clustering algorithm to facilitate de novo repeat identification without the need for reference databases of known elements. Because the algorithm uses short sequences randomly sampled from the genome as input, it is ideal for analyzing next-generation sequence reads.
A de novo repeat assembly method that avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real Drosophila melanogaster NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.
Assembles a set of transposable elements directly from the reads. Tedna uses Illumina paired-end reads, the most widely used sequencing technology for de novo assembly, and forms full-length transposable elements. Tedna can be used on standard computers with limited RAM resources, although it may also use large memory for better results. Most of the code is parallelized and thus ready for large infrastructures.
A command line application to annotate transposable elements from paired-end whole genome shotgun data. There are many tools to estimate the mathematical nature of repeats from short sequence reads. There are also a number of tools for analyzing repeats directly from a genome assembly. This tool allows you to infer the abundance of repeat types in the genome without a reference genome sequence. The output files make it easy to quickly summarize genomic abundance by transposable element class, superfamily, family, or any other level of the repeat taxonomy.
Assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. REPdenovo is a powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families.
Provides a fully automated rationally derived method for complete analysis of significant Common Insertion Sites (CISs) using next generation sequencing. TAPDANCE furnishes a pipeline that performs raw sequence processing and trimming, mapping to the reference genome, CIS identification, and nearest-gene annotation. The software can be applied to many sequence sampling depth and allows to manage large dataset.
Facilitates transposable elements consensus sequences curation. ReannTE provides scriptsthat simplifies merging two consensus libraries and parses the masking outputs to evaluate overlaps. It was used to eliminate non-TE repeats (simple repeats or gene 120 families).
Assists in the identification of protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. TransposonPSI can be used to detect potential transposon open reading frames (ORFs) within a protein set, or regions of transposon homology within a larger genome sequence. This method can be applied for identifying mobile elements across eukaryotes including protozoa, plants, fungi, and animals.
Obsolete
A bioinformatic pipeline dedicated to find, annotate and quantify transposable elements as well as other repeated DNA, in NGS low coverage genomic datasets. dnaPipeTE produces a global estimation of the main proportion of repeat classes in the genome. It estimates the relative abundance of each assembled repeat and draws the TE age distribution for the most recent elements.
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Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing
Tools (4):
Circos, Trimmomatic, RepeatExplorer, RepeatMasker
Topics (3):
WGS analysis, De novo sequencing analysis, Gossypium hirsutum
De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust
Tools (4):
tRNAscan-SE, EVM, BLASTP, TransposonPSI
Topics (1):
De novo sequencing analysis
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
Tools (4):
GenomeTools, TransposonPSI, RepeatMasker, GeneMark
Topics (1):
WGS analysis
Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum
Tools (4):
FastUniq, Trimmomatic, RepeatExplorer, BLASTN
Topics (3):
WGS analysis, De novo sequencing analysis, Saccharum officinarum
In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae
Tools (3):
RepeatExplorer, BLASTN, BLASTX
Topics (3):
De novo sequencing analysis, WGS analysis, Genome annotation
Well characterized sequence features of eukaryote genomes and implications for ab initio gene prediction
Tools (3):
RepeatMasker, PILER, RepeatExplorer
Topics (3):
WGS analysis, De novo sequencing analysis, Genome annotation
Repeat Composition of CenH3 chromatin and H3K9me2 marked heterochromatin in Sugar Beet (Beta vulgaris)
Tools (3):
RepeatExplorer, BLASTN, BLASTX
Topics (3):
De novo sequencing analysis, WGS analysis, Genome annotation
Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa
Tools (5):
RepeatExplorer, BLASTN, BLASTX, Clustal W, Geneious
Topics (3):
WGS analysis, De novo sequencing analysis, Genome annotation
An Exploration into Fern Genome Space
Tools (3):
FASTX-Toolkit, RepeatExplorer, RepeatMasker
Topics (2):
WGS analysis, De novo sequencing analysis
The de novo genome assembly and annotation of a female domestic dromedary of North African origin
Tools (3):
RepARK, Velvet, QUAST
Topics (1):
De novo sequencing analysis
Genome Anatomy of Pyrenochaeta unguis hominis UM 256, a Multidrug Resistant Strain Isolated from Skin Scraping
Tools (6):
GeneMark, Blast2GO, InterProScan, RNAmmer, tRNAscan-SE, TransposonPSI
Topics (1):
De novo sequencing analysis
Independent Domestication of Two Old World Cotton Species
Tools (3):
Trimmomatic, RepeatExplorer, RepeatMasker
Topics (6):
WGS analysis, De novo sequencing analysis, Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum, Gossypium herbaceum
Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non coding regions
Tools (6):
MEGA, EMBOSS, Jellyfish, Tedna, TEclass, CLC Genomics Workbench
Topics (2):
WGS analysis, De novo sequencing analysis
Recent and dynamic transposable elements contribute to genomic divergence under asexuality
Tools (4):
RepeatExplorer, Trinity, Bowtie2, RSEM
Topics (5):
WGS analysis, De novo sequencing analysis, Taraxacum officinale, Leukemia, Lymphoproliferative Disorders
Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives
Tools (8):
FASTX-Toolkit, cutadapt, BWA, SAMtools, RepeatExplorer, Geneious, BLASTN, Jellyfish
Topics (7):
WGS analysis, De novo sequencing analysis, Zea mays, Zea mays subsp. parviglumis, Zea diploperennis, Zea luxurians, Tripsacum dactyloides
Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374
Tools (5):
PRINSEQ, Velvet, ABACAS, PGAP, TransposonPSI
Topics (1):
De novo sequencing analysis
Genome Wide Analysis of Repeat Diversity across the Family Musaceae
Tools (8):
RepeatExplorer, RepeatMasker, BLASTX, BLASTN, SeaView, FigTree, MAFFT, FastTree
Topics (1):
De novo sequencing analysis