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This process will produce a resultant VCF file, a tab-separated text file in a tabular like structure, containing genetic variants as rows. This file can then be used as input into the ANNOVAR software program for the variant annotation process, outputting interpretations of the variants identified from the upstream bioinformatics pipeline.
The broad goals of the projects are to: Provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data.; Facilitate the inclusion of biological metadata in the analysis of genomic data, e.g. literature data from PubMed, annotation data from LocusLink/Entrez.
It has a tier-based data model that supports multi-level, multi-participant annotation of time-based media. It is applied in humanities and social sciences research ( language documentation , sign language and gesture research ) for the purpose of documentation and of qualitative and quantitative analysis. [ 3 ]
Single nucleotide polymorphism annotation (SNP annotation) is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query.
Understanding the function of genes and their products in the context of cellular and organismal physiology is the goal of process-level annotation. An obstacle of process-level annotation has been the inconsistency of terms used by different model systems. The Gene Ontology Consortium is helping to solve this problem. [27]
In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome, [2] by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. [3]
It is part of the AgBase database of curated, publicly accessible suite of computational tools for GO annotation and analysis. [12] Following annotation, KEGG (Kyoto Encyclopedia of Genes and Genomes) enables visualization of metabolic pathways and molecular interaction networks captured in the transcriptome.
SnpEff is an open source tool that performs annotation on genetic variants and predicts their effects on genes by using an interval forest approach. This program takes pre-determined variants listed in a data file that contains the nucleotide change and its position and predicts if the variants are deleterious.