SeqFeatR for the Discovery of Feature-Sequence Associations

PloS One
Bettina BudeusDaniel Hoffmann

Abstract

Specific selection pressures often lead to specifically mutated genomes. The open source software SeqFeatR has been developed to identify associations between mutation patterns in biological sequences and specific selection pressures ("features"). For instance, SeqFeatR has been used to discover in viral protein sequences new T cell epitopes for hosts of given HLA types. SeqFeatR supports frequentist and Bayesian methods for the discovery of statistical sequence-feature associations. Moreover, it offers novel ways to visualize results of the statistical analyses and to relate them to further properties. In this article we demonstrate various functions of SeqFeatR with real data. The most frequently used set of functions is also provided by a web server. SeqFeatR is implemented as R package and freely available from the R archive CRAN (http://cran.r-project.org/web/packages/SeqFeatR/index.html). The package includes a tutorial vignette. The software is distributed under the GNU General Public License (version 3 or later). The web server URL is https://seqfeatr.zmb.uni-due.de.

References

Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Sep 19, 2009·Nature Reviews. Genetics·Matthew Stephens, David J Balding
Apr 27, 2010·PLoS Computational Biology·Jan Nikolaj DybowskiDaniel Hoffmann
Mar 8, 2011·Gastroenterology·Marianne RuhlEast German HCV Study Group
Nov 23, 2011·Proceedings of the National Academy of Sciences of the United States of America·Faruck MorcosMartin Weigt
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Apr 27, 2013·Bioinformatics·Nancy F HansenJames C Mullikin
Jun 13, 2013·Methods in Molecular Biology·Miguel E RenteríaSarah E Medland
Sep 7, 2013·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Christopher G ChuteJyotishman Pathak
Oct 31, 2013·Methods in Molecular Biology·Fabian Sievers, Desmond G Higgins
Feb 14, 2014·Nature·Regina Nuzzo
Aug 15, 2014·BioData Mining·Dominik HeiderDaniel Hoffmann
Feb 28, 2015·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Helenie KefalakesJoerg Timm
Nov 5, 2015·Nature·Charlie Schmidt

Related Concepts

Bayesian Prediction
Computer Programs and Programming
Sequence Determinations, DNA
Twitter Messaging
Genome
HLA Antigens
Computer Software
Viral Proteins
Epitopes, T-Lymphocyte
Patterns

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.