Work

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

Year: 2016

Type: article

Abstract: As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. AVAILABILITY AND IMPLEMENTATION: ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btw593

Authors: Aaron M Rosenfeld, Wenzhao Meng, Eline T Luning Prak, Uri Hershberg

Institutions: Drexel University, University of Pennsylvania

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Cancer Institute, National Institute of Allergy and Infectious Diseases

Awards: G2572619169, Tissue compartmentalization of human lymphocytes, Abramson Cancer Center Support Grant