MUTATION_SCHEMES

CHARGE_MUTATIONS

HYDROPATHY_MUTATIONS

POLARITY_MUTATIONS

VOLUME_MUTATIONS

Definitions of replacement (R) and silent (S) mutations for different amino acid
physicochemical classes.

Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.

Susanna Marquez

shazam

Immunoglobulin Somatic Hypermutation Analysis

Mohamed Uduman

Namita Gupta

Julian Zhou

Nima Nouri

Noah Yann Lee

Ang Cui

Jason Vander Heiden

Gur Yaari

Steven Kleinstein

MUTATION_SCHEMES function

A MutationDefinition object defining:<ul>
<li><code>CHARGE_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain charge class.</li>
<li><code>HYDROPATHY_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain hydrophobicity class.</li>
<li><code>POLARITY_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain polarity class.</li>
<li><code>VOLUME_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain volume class.</li>
</ul>

Format

Amino acid mutation definitions — MUTATION_SCHEMES

Amino acid mutation definitions

MUTATION_SCHEMES: Amino acid mutation definitions

Description

Arguments

Format

References