Clarke van Steenderen

Clarke van Steenderen

PhD student in the Department of Zoology and Entomology, Centre for Biological Control, Rhodes University

Download multiple GenBank sequences from R

1 minute read

Published:

Perhaps a published paper lists their GenBank accession numbers as a range; for example KC664779 - KC665461. In R, one can use the following code to download all the sequences in this range, and save them as a FASTA file:

start = 664779
end = 665461

# create an empty vector to store the sequences
desired_sequences = c()

# run a loop to generate all the sequence IDs
k = 0
for (i in start:end){
  desired_sequences[k] = paste("KC", i, sep = "")
  k = k + 1
}

# access the GenBank sequences in the list using the ape read.GenBank function
output = ape::read.GenBank(desired_sequences)
# store the GenBank sequences as a FASTA file
ape::write.dna(output, file ="my_seqs.fasta", format = "fasta", append = FALSE, nbcol = 6, colsep = "", colw = 10)

Otherwise, you can specify particular accession numbers in a predefined list, as shown below. These accession numbers are all the COI and 28S sequences from the hymenopterans in the study by Chen et al. 2004.

# 28S sequences
desired_seqs_28S = c("AY317172", "AY317173","AY317170", "AY317164", "AY317169", "AY317160", "AY317155", "AY317171", "AY317163", "AY317178", "AY317175", "AY317166", "AY317162", "AY317168", "AY317176", "AY317179", "AY317181", "AY317167", "AY317159", "AY317158", "AY317157", "AY317174", "AY317180", "AY317156", "AY317161", "AY317165", "AY317177")

eurytomid_28S = ape::read.GenBank(desired_seqs_28S)

ape::write.dna(eurytomid_28S, file = "eurytomids_28S_genbank.fas", format = "fasta", append = F)

# COI sequences
desired_seqs_coi = c("AY317223", "AY317226", "AY317239", "AY317227", "AY317233", "AY317225", "AY317236", "AY317224", "AY317235", "AY317238", "AY317228", "AY317222", "AY317232", "AY317230", "AY317231", "AY317234", "AY317242", "AY317229", "AY317243", "AY317240", "AY317241", "AY317221")

eurytomid_coi = ape::read.GenBank(desired_seqs_coi)

ape::write.dna(eurytomid_coi, file = "eurytomids_COI_genbank.fas", format = "fasta", append = F)

Multiple sequence alignment Fasta file manipulation

6 minute read

Published:

This bit of code can be a great help to subset a Fasta file alignment based on certain conditions taken from a sample information file (e.g. subset only the samples collected in Spring, or those in Winter and greater than y cm, or everything except those in Autumn, etc.).

Plot a phylogeny in R using ggtree

2 minute read

Published:

This post will show you how to generate a phylogeny plot in R, with a heatmap alongside it. This example uses binary data, but it can be adapted to be plotted with a continuous variable.

Creating a climate map with GPS coordinate points

3 minute read

Published:

This R code shows you how to plot a map for a desired country or geographic region, and how to display a chosen climatic variable (e.g. mean annual temperature, annual precipitation) as an overlay. The WorldClim dataset has 19 variables to choose from.

Creating an elevation map with GPS coordinate points

less than 1 minute read

Published:

This R script plots the map of a desired country, and colours it by elevation. It then adds GPS coordinate points to it (for example sampling sites) from an Excel file. Check out the final image at the bottom of this post 😃. The North arrow and Tetramesa wasp was added manually later in Inkscape.