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.
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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.
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 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 (5):
Circos, Trimmomatic, RepeatExplorer, RepeatMasker, Repbase
Topics (3):
WGS analysis, De novo sequencing analysis, Gossypium hirsutum
Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies
Tools (4):
TBLASTN, dnaPipeTE, jModelTest, PhyML
Topics (2):
WGS analysis, De novo sequencing analysis
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 (6):
tRNAscan-SE, EVM, BLASTP, TransposonPSI, UniProtKB, Repbase
Topics (1):
De novo sequencing analysis
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
Tools (6):
GenomeTools, TransposonPSI, RepeatMasker, GeneMark, UniProtKB, Repbase
Topics (1):
WGS analysis
Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests
Tools (8):
Musket, PRINSEQ, COPE, Bowtie2, RepARK, BLASTN, SOAPdenovo, Blast2GO
Topics (2):
De novo sequencing analysis, Boswellia sacra