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BLAST / Basic Local Alignment Search Tool

Allows to align query sequences against those present in a selected target database. BLAST is a suite of programs, provided by NCBI, which can be used to quickly search a sequence database for matches to a query sequence. The software provides an access point for these tools to perform sequence alignment on the web. The set of BLAST command-line applications is organized in a way that groups together similar types of searches in one application.

PLACNET / PLAsmid Constellation NETwork

Identifies, visualizes and analyzes plasmids in whole genome sequencing (WGS) projects by creating a network of contig interactions. PLACNET uses three types of information to identify plasmids: (i) information about scaffold links and coverage in the WGS assembly, (ii) comparison to reference plasmid sequences, and (iii) plasmid-diagnostic sequence features such as replication initiator proteins.

Determines bacterial plasmid sequences in genomic and metagenomic assemblies. PlasFlow is an open source software, based on a deep neural network model that distinguishes plasmids and chromosomes. It can be applied to any assembly, including those without raw sequencing data. The program can be used for: (i) predicting phyla and supplying information related to taxons contributing to the plasmidome in a given environment (ii) identifying plasmid sequences carrying genes involved in heavy-metal resistance, (iii) analyzing large plasmids and megaplasmids.

A software tool for assembling plasmids from whole genome sequencing data. plasmidSPAdes utilizes SPAdes for transforming the de Bruijn graph into the assembly graph and finds a subgraph of the assembly graph that we refer to as the plasmid graph. It further uses ExSPAnder for repeat resolution in the plasmid graph using paired reads and generates plasmidic contigs. plasmidSPAdes does not require any specialized sample preparation to isolate plasmids, it has a potential to increase the throughput of plasmid discovery. It thus complements the recently published approach that is mainly aimed at analyzing plasmids after plasmid isolation.

Allows identification of plasmids in total or partial sequenced isolates of bacteria. PlasmidFinder is based on a curated database of plasmid replicons intended for the identification of plasmids in whole-genome sequences originating from Enterobacteriaceae species. The web application provides the detection of replicons in the whole genome sequencing (WGS) but also assigns the plasmids under study to lineages that trace back the information to the existing knowledge on Inc groups and suggests possible reference plasmids for each lineage.

Enables the detection of plasmids from bacterial whole genome sequencing (WGS) data without read assembly. PlasmidSeeker is a tool that allows detection of known plasmid sequences from unassembled raw WGS reads. Moreover, this tool is able to estimate copy numbers of these known plasmids and is suitable to utilize as a first step in the analysis of plasmid content.

A tool designed for extracting circular sequences from de novo assembly graphs. Recycler can be applied on isolate as well as metagenome and plasmidome data. The circular sequences it outputs may be plasmids, phages, etc. Recycler uses only features of the assembly graph (contig overlaps, lengths, and coverage level information) and alignments of paired-end reads to the contigs in the graph in order to identify these sequences.

Plasmid Profiler

Provides comparative plasmid content analysis. Plasmid Profiler is a comparative pipeline for visualization of plasmid content in whole genome sequencing (WGS) data from bacterial isolates. It identifies plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. Users can query plasmids for genes or regions of interest and visualize results as an interactive heat map.

Assists in heterologous candidate enzymes selection. Selenzyme is an online tool which query a target reaction. It can accept multiple queries from any other web-based application. It provides enzyme selection solutions in different scenarios such as the selection of enzyme sequences.

Identifies sequence representing mobile genetic elements (MGEs). PlasmidTron is a tool that utilizes the phenotypic data such as antibiograms, virulence factors, or geographic information. It can be used to assemble reads from each sample linked by a phenotype. This tool allows users to reconstruct all of the sequences of plasmid responsible for a particular phenotype.

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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

Rodrigo Bacigalupe

microbiologist UZFG AVCR

BLAST RDP BlastKOALA

Carmen Carrasquilla

Tech Transfer Officer McMaster University - Industry Liaison Office

seer BTyper ResFinder

Metagenomics and RNA biology Institute of Biochemistry and Biophyscis PAS, Warsaw, Poland

I am interested in the analysis of all kinds of NGS data, but focused mostly on metagenomics (as it is a subject of my PhD Studies) and RNAseq

PlasFlow

Mamitina Alain Noah RABENANDRASANA

Genomic of antimicrobial resistant bacteria Institut Pasteur of Madagascar

Mass-Up Motif discovery pipeline PlasFlow

Plasmid identification software tools | Shotgun metagenomic sequencing data analysis

Plasmids have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their extraction through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing.

Source text:
(Rozov et al., 2016) Recycler: an algorithm for detecting plasmids from de novo assembly graphs. Bioinformatics.

Parent category

Metagenomic sequencing analysis

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