Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Analyses genomic DNA and Protein sequence. Dotter provides a tool to explore the visual appearance of this landscape, as well as a tool to examine the sequence alignment it represents. It runs linear in space so has no practical limit for the length of sequences. The user can 'play' with the min and max cutoffs until achieves the optimal separation between noise and signal. The tool can be used for displaying dot-matrices generated by other programs. The software is a part of the Seqtools toolkit.
Allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Gepard utilizes suffix arrays for rapid heuristic dotplot calculation. For large dotplots it searches exact word matches of a certain length (10 by default) from one sequence in the suffix array of the other sequence. As an arbitrary word is found in log(n) time within a suffix array this method reduces complexity of the dotplot calculation from O(m*n) to O(m * log n) (where n is the length of the longer, m the length of the shorter sequence). For small dotplots the classical window-based dotplot calculation is utilized.
Generates publication-ready figures for complex sequences. Flexidot is a multi-purpose dotplot tool for publication-ready dotplots, pairwise, handling self and all-against-all comparisons with individual and combined visualizations. This software transforms detected matches in diagonals and creates clear vector images or standard raster graphics. It suits for identification of conserved motifs in related sequences and evaluation of tandem repeat higher order structures of error-prone long reads.
Allows comparison of two genomes. D-Genies uses the nucleic sequence alignment program called minimap2, and produces dot plots for nucleic sequences. The software has been developed to process large genomes, but it is also suited for small or medium size genomes. It is able to produce a complete human vs chimpanzee genome dot plot in one hour and 10 min. D-Genies can be extended with new aligners and new alignment file formats.
Provides a set of programs for sequence alignments visualization. SeqTools is a web-based tool that is composed of three components: (i) Blixem is a browser for one-to-many alignment; (ii) Dotter offers a graphical program to compare two sequences and; (iii) Belvu allows users to view and edit multiple sequence alignments and phylogenic trees in a wide range of formats.
Compares easily virus genomes. GenomeDiff is a free, open-source software that allows to compare virus genomes visually by dotplot. It uses alignment view and compare, for example, Hiv-1 & Visna. Locate p24 within Hiv-1. This software can also be used to compare natural language texts. Finally, it exports diagram as PDF.
Makes a dot-plot with the output file from Compare or StemLoop. Dotplot(+) generates dot-plots of the points of similarity between two sequences. It calculates the minimum density in bases per 100 platen units along either axis that would allow all of the points to be plotted on a single page. The density can be selected and the software divides the plot into as many pages as it takes to plot the whole file.
Explores data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system. It offers a vectorized function to convert one-letter amino-acid code into the three-letter one, for instance "A" into "Ala", a function to converts an alignment into a matrix of characters, a function that tries to estimate the baseline value for relative fluorescence units (RFU) data from capillary electrophoresis with the heuristic that the most common value is the baseline and many others.
Compares sequences by the diagonal plot method. Dotlet is designed to be an independent platform and to run in a Web browser, thus enabling the majority of researchers to use it. Sequences can be imported by cut-and-paste (there is no built-in limit to the number of sequences that can be imported), and menus allow the user to select which two sequences to compare. Dotlet supports protein versus protein, DNA versus DNA, and mixed comparisons.
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/).