Locus-specific variation data | DNA annotation - OMICtools

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LOVD / Leiden Open Variation Database

Provide a flexible, freely available tool for Gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes. LOVD allows users to link large numbers of DNA variants in one or more genes to an individual (multi-gene disorders or large scale next-generation sequencing). You can even use LOVD on your personal computer to browse through the variants in your own exome/genome. To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer.

UMD TP53 database

A reference for all scientists working on p53, including information on p53 structure and function, the description of all p53 monoclonal antibodies and the phylogenetic analysis of p53. More than 50% of human tumors carry TP53 gene mutations and in consequence more than 45,000 somatic and germline mutations have been gathered in the UMD TP53 database. Analyses of these mutations have been invaluable for bettering our knowledge on the structure-function relationships within the TP53 protein and the high degree of heterogeneity of the various TP53 mutants in human cancer.

TREAT-NMD DMD Global Database

A joined international effort through the TREAT-NMD network to provide up-to-date information about mutations of the Duchenne muscular dystrophy (DMD) gene identified in patients with dystrophinopathies worldwide. Published and unpublished molecular data are collected from more than 30 national registries. TREAT-NMD DMD Global Database aims at making the information readily accessible to non-commercial users (geneticists, clinicians or researchers) interested in the genetic variations of the DMD gene, the clinics of dystrophinopathies, or the development of new therapeutic approaches.

Provides information about mutations of the APC gene. The UMD- APC database aims at making the information readily accessible to anyone interested in the genetic variations of the APC gene, and to provide an easy way for those who investigate these variations to report their most recent findings. It has been enriched with germline variations found through genetic testing analyses provided by the French APC network of 8 diagnostic laboratories that register up-to-date information about mutations in genes involved in colorectal cancer predisposition. This database currently contains published and unpublished information about the APC variations reported in French diagnostic laboratories.

amamutdb.no / alpha-mannosidosis mutation database

A publicly accessible online resource for recording and analyzing MAN2B1 variants. amamutdb.no offers structured and relational information on MAN2B1 mutations and genotypes along with associated clinical phenotypes. The following information is freely available as a service to the scientific community: Published data on disease causing mutations and benign polymorphisms and their effect on enzyme activity, protein conformation, processing and localization. Clinical and demographic data are available as statistical summaries. Sensitive information and unpublished data are protected.

Gathers information concerning C1-INH gene mutation. HAEdb aims to assist users in the comprehension of information on genetic alterations of the C1-INH gene. The data contained on this database can be searched and compared according to several characteristics such as type, size, or mutation. It intends to be a useful resource to determine if a new mutation may be disease-causing or not.

EURO-WABB locus specific database

Provides catalogues of gene variations involved in monogenic diabetes syndromes. The EURO-WABB locus specific database is an online resource that operates at a disease specific level to support efficient diagnosis and research for these syndromic diabetes diseases. This database has also links to other services such as PubMed, HGNC, Entrez Gene, OMIM and GeneCards, in addition to sequence databases.

KGDB / Kidney gene database

Catalogues information about genes implicated in kidney disease. KGDB is a curated and integrated database that provides a wealth of relevant information. Provided data were extracted from publications in the biomedical literature and from gene expression databases. This resource can be queried by gene names, symbols, aliases and identification numbers, such as LocusLink ID or UniGene ID. It can also be browsed by molecular event or specific kidney disease.

LSDBs / Locus-Specific DataBases

Links towards databases dealing with the information relative to gene sequence variation associated with human phenotypes. LSDBs aims to propose a registry as exhaustive as possible of online resources available. Each recorded repository includes data such as a direct URL for accessing the targeted repository, curators name, the possible linked diseases, and the acceptance of submission by external users as well as the last update date.

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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

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