seqUtils

Utilities for working with biological sequences in R.

Overview

seqUtils provides simple, efficient tools for common sequence analysis tasks:

• Read/write FASTA files - Fast I/O for single-line and multi-line FASTA formats
• Translate sequences - DNA/RNA to amino acids with deletion handling
• Align sequences - Wrapper for MAFFT alignment to reference sequences
• Find substitutions - Compare sequences and identify differences
• Calculate consensus - Generate consensus sequences from alignments
• Clean sequences - Remove or replace non-standard characters

Installation

You can install the development version of seqUtils from GitHub with:

# install.packages("devtools")
devtools::install_github("SamT123/seqUtils")

Example

library(seqUtils)

# Read FASTA file
sequences <- fast_fasta("sequences.fasta")

# Translate to amino acids
aa_sequences <- translate(sequences)

# Find substitutions compared to a reference
substitutions <- get_substitutions(
  reference_seq,
  query_seqs,
  exclude = c("X", "N")
)

Requirements

• Biostrings package
• MAFFT (for alignment functions)