alignment: Sample Alignment

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This is an alignment for seq_var package.

Usage

data(alignment)

Format

An alignment with sequence ID being formatted as follows: genus_name:accession:genus:species:strain_info/seqBegin-seqEnd. The location of each party can be rearranged, and the separator can be other speciall characters, such as "|".

Source

Wen Chen

Examples

data(alignment)
str(alignment)
alignment

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
 'DNAbin' raw [1:17, 1:883] - - - - ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:17] "Claviceps:gb_EF052276:Claviceps:fusimis:no_strain_info/1-585" "Claviceps:gb_FJ686007:Claviceps:setariicola:no_strain_info/1-532" "Claviceps:gb_FJ686005:Claviceps:truncatispora:isolate_CCC_578/1-565" "Claviceps:gb_EF057431:Claviceps:setariicola:isolate_CCC793/1-532" ...
  ..$ : NULL
17 DNA sequences in binary format stored in a matrix.

All sequences of same length: 883 

Labels:
Claviceps:gb_EF052276:Claviceps:fusimis:no_strain_info/1-585
Claviceps:gb_FJ686007:Claviceps:setariicola:no_strain_info/1...
Claviceps:gb_FJ686005:Claviceps:truncatispora:isolate_CCC_57...
Claviceps:gb_EF057431:Claviceps:setariicola:isolate_CCC793/1...
Claviceps:gb_EF057430:Claviceps:tenuispora:isolate_CCC853/1-...
Claviceps:gb_EF057428:Claviceps:langdonii:isolate_CCC820/1-5...
...

Base composition:
    a     c     g     t 
0.230 0.314 0.256 0.200 

RAM documentation built on May 2, 2019, 3:04 p.m.