SeqFeatR

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.

SeqFeatR for the Discovery of Feature-Sequence Associations.

SeqFeatR is a web-based tool for identifying associations between mutation patterns in protein sequences. The SeqFeatR algorithm uses frequentist and Bayesian methods.

SeqFeatR

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