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Title: Visualizing Sequence Alignment by Generating Publication-Ready Plots
Version: 0.1
Author: Mohamed Soudy [aut, cre]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Description: Providing publication-ready graphs for Multiple sequence alignment. Moreover, it provides a unique solution for visualizing the multiple sequence alignment without the need to do the alignment in each run which is a big limitation in other available packages.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.2
Imports: ggplot2, ggmsa, reshape2
NeedsCompilation: no
Packaged: 2023-06-13 18:43:32 UTC; Soudy
Repository: CRAN
Date/Publication: 2023-06-14 16:22:05 UTC

Convert string to a character vector

Description

convert string that can be DNA or protein sequence to a character vector

Usage

Seqtochar(x)

Arguments

x

a sequence of DNA or Protein

Value

this function is mainly used by ggaligner function to convert the input sequence to character vector

Author(s)

Mohamed Soudy Mohmedsoudy2009@gmail.com

Examples

Seqtochar("ATGACATAAT")


Visualize the alignment object from msa package

Description

Generating a plot for msa object of DNA or Protein sequence

Usage

ggaligner(alignment,start=1,end=10,color="Clustal",font="helvetical",label_font = 12)

Arguments

alignment

alignment object returned from msa package

start

start position of the desired alignment region

end

end position of the desired alignment region

color

color scheme to use ex: Clustal, Chemistry_AA, Shapely_AA

font

font family to use ex: helvetical, TimesNewRoman

label_font

font size of sequence names

Value

An enhanced plot for the alignment using ggplot2 and ggmsa packages

Author(s)

Mohamed Soudy Mohmedsoudy2009@gmail.com

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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