SeededAlignment.jl

SeededAlignment.jl aims to provide a frameshift robust framework for codon alignments. It can support downstream analyses such as selection detection, phylogenetic inference, and evolutionary modeling. The package is design to be flexible and performant enough for large-scale codon alignments.

Installation

You can install this package using Julia's package manager:

using Pkg
Pkg.add(url="https://github.com/MurrellGroup/SeededAlignment.jl")

---

Core Methods

-seed_chain_align - frameshift robust seed-and-chain strategy for codon alignment. Significantly faster than nw_align on biologically meaningful data.

-msa_codon_align - frameshift robust codon-level MSA (visual) constructed by scaffolding pairwise codon alignments against a trusted reference.

-clean_frameshifts - cleans pairwise (or multiple) sequence alignments of frameshift errors if they contain a trusted reference.

-nw_align - frameshift robust codon-level Needleman-Wunsch algorithm that detects and cleans frameshift errors.

Note: nw_align and seed_chain_align also support De-Novo nucleotide alignments.

FASTA Support – read_fasta / write_fasta

---

Examples

seed_chain_align

---

This is the main method for computing pairwise codon alignments.

using SeededAlignment

seq_names, dna_seqs = read_fasta("example.fasta")
# this sequence has no frameshift errors - reference sequence
ref_CDS = dna_seqs[1]
# this sequence might have frameshift errors - query sequence
query_CDS = dna_seqs[2]
# compute codon alignment by cleaning frameshift errors
codon_alignment = seed_chain_align(ref=ref_seq, query=query_seq)

If we want to view what was cleaned up in prinouts we can run the last line again with the verbose kwarg

codon_alignment = seed_chain_align(ref=ref_seq, query=query_seq, verbose=true)

---

clean_frameshifts

---

In the situation where we have a pairwise alignment that has a broken reading frame due to frameshift errors. We can clean up the frameshift errors if one of the sequences is a trusted reference sequence.

using SeededAlignment

# read in raw_alignment that contains frameshift errors
seq_names, raw_alignment = read_fasta("alignment_frameshift_error.fasta")
# aligned reference sequence that is frameshift free
aligned_ref = raw_alignment[1]
# aligned query sequence that contains frameshift errors
aligned_query = raw_alignment[2]
# cleans up frameshift errors
cleaned_alignment = clean_frameshifts(aligned_ref, aligned_query)
# write the clean result to fasta file
write_fasta("cleaned_codon_alignment.fasta", cleaned_alignment, seq_names=seq_names)

By default the changes are visibile in printouts just like seed_chain_align with verbose kwarg.

---

msa_codon_align

---

This method produces a reference-guided codon multiple sequence alignment that is frameshift robust. This might be helpful because traditionally if a single sequence in the alignment contains a frameshift error it breaks the entire codon alignment and one would have to currate a correction manually.

using SeededAlignment

# read in dna_sequences
seq_names, dna_seqs = read_fasta("example.fasta")
# choose a reference sequence with intact reading frame
ref_seq = dna_seqs[1]
# extract the query sequences
query_seqs = dna_seqs[2:end]
# produce a codon alignment based on the reference sequence reading frame
msa_codon_alignment = msa_codon_align(ref_seq, query_seqs)
# write alignment to fasta file
write_fasta("example_output.fasta", msa_codon_alignment, seq_names = seq_names)

Note that the resulting alignment will be biased by the reference sequence and might need to be supplemented if the intended alignment is complex.