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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.

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.

RepARK / Repetitive motif detection by Assembly of Repetitive K-mers

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.

Identifies bacterial insertion sequences (ISs) and their sequence elements-inverted and direct repeats-in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours, making it a valuable high-throughput tool for a global search of IS elements.

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.

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.

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Big data scientist National institute of Plant Gneome Reseaech (NIPGR)

Research Interests Gene fusion detection in Plants Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants. Whole genome and transcriptome sequencing data analysis of Plants In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants. Development of webservers, databases and computational pipelines for plant research Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research. Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies. Professional & Academic Background Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India Awards and Fellowships Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009 Scientific Contributions/ Recognitions Associate editor: Journal of Translational Medicine. Editorial Board Member of Journal: Theoretical Biology and Medical Modelling. Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals. Web Resources/ Databases (Developed/ Contributed) A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/) GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/). Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/). Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/). Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/). Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/). Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/) Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/). A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).

FusionFinder comrad

Mahantesh Biradar

‎Graduate PhD researcher focusing on Cardiovascular Epidemiology & Social Media Enthusiast Research Stash

I'm a Graduate PhD researcher in the area of Biomedical Science and focussing on the Pharmacogenomics/Pharmacogenomics of Diabetes and related complications

Transposable element annotation software tools | De novo genome sequencing data analysis

Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the "repeatome" during genome-wide analysis often poses a challenge.

Source text:
(Goubert et al., 2015) De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). Genome Biol Evol.

Parent category

De novo sequencing analysis

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