README.md

In MichelleMengzhi/hmtp: Homology Modeling Templates Preparation

hmtp

The goal of hmtp is to prepare templates for homology modeling. This package can pick out less than 5 best protein sequences that can do homology modling with target sequence as templates from given database based on pairwise alignment. The alignment files for picked templates and target protein, and pdb file of templates are generated/downloaded to users for homology modeling. This package also provide a rough visualization of how similar two provided aligned proteins are in both 1D and 3D. The highlight of this package is that currently there is no R package which can generate 3D alignment structure of given proteins which is a indeed helpful visualization for homology modeling and other bioinformatics work flow after paiwise alignments.

Installation

You can install the released version of hmtp from github with:

library(devtools)
install_github("MichelleMengzhi/hmtp", build_vignettes = TRUE)
library(hmtp)

To run the shinyApp:

runHmtp()

Overview

browseVignettes("hmtp") 

This package contains two main functions: selectTemplates which selects templates for the target in the later homology modeling and gets their pdb files and alignment file, alignment3dVisualization whcih provides a visualization of how similar the template and target sequences are in 3D, helper functions crossReferenceList, GetPdbFileGenerator, pathGeneratorMovement, which contribute in main functions but can also be used separately.

Contrbutions

lsf.str("package:hmtp")

The author of the package is Yuexin Yu.

In selectTemplates function, Biostrings, DECIPHER packages are imported for capturing protein sequences from fasta file and 1D visualization respectively. Yuexin Yu built up the filter to capture information for pairwise alignment, the html download of selected pdb files, and the generation of alignment files for later homology modeling.

In alignment3dVisualization function, rgl package is used to help to generate a line plot graph. Yuexin Yu built up the filter to capture the xyz coordinates from the input and output a 3D image which plots two set of data and line all points all to generate a rough 3D structure of proteins.

Example

You can use example data in the package with the following code

selectTemplates("targetExample.fasta", "databaseExample.fasta", "databaseExample.txt")

which generates tio 5 pairwise sequence alignments and visualization of the first argument as the target sequence and the second argument as the protein database.

alignment3dVisulization("align.pdb", "4GSA", "5TE2")

which generates a quick 3D visualization of the alignment of the second and third arguments

References

H. Pages, et al. Efficient manipulation of biological strings. Rereieved from https://www.bioconductor.org/packages/devel/bioc/manuals/Biostrings/man/Biostrings.pdf

E. Wright. DECIPHER. Retrieved from https://bioconductor.org/packages/release/bioc/html/DECIPHER.html

D. Adler, et al. 3D Visualization Using OpeGL. Retreived from https://cran.r-project.org/web/packages/rgl/rgl.pdf

MichelleMengzhi/hmtp documentation built on Dec. 12, 2019, 12:54 a.m.