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Codon-aware MSA

This set of scripts facilitates creating in-frame multiple sequence alignments (MSA) from coding nucleotide sequences, only some of which are in frame. It requires the use of a general MSA program (e.g., muscle or MAFFT) that can handle aligning protein sequences. The workflow is as follows

  1. Obtain coding sequences (nucleotides). At least one of them must be in frame
  2. Run these sequences through pre-msa.bf in order to correct frame-shift mutations and translate the resulting sequences to proteins.
  3. Take the output of step 2 and run in through the general MSA program to generate a protein MSA
  4. Run the protein MSA and the frameshift corrected nucleotide sequences from step 2 through post-msa.bf to obtain a nucleotide msa. This step will also, optionally, compress all identical sequences, i.e. replace them with a single representative sequence.

For step 2, you can use --E number (where number is a small floating point value e.g. 0.05) command line option to permit the alignment of sequences with low homology if you see warning messages about sequences that could not be aligned.

Example

[1]. Coding sequences (unaligned) in example.fas.

[2]. hyphy pre-msa.bf --input example.fas

Analysis Description
--------------------
 Load nucleotide sequences (SOME of which **must be in frame**), perform
frameshift correction as needed, and translate to amino-acids for
subsequent alignment. 

- __Requirements__: Sequences

- __Citation__: TBD

- __Written by__: Sergei L Kosakovsky Pond

- __Contact Information__: spond@temple.edu

- __Analysis Version__: 0.01

code: Universal
input: example.fas
[Data QC] Loaded 28 sequences on 2669 sites from **/Users/sergei/Development/hyphy-analyses/codon-msa/example.fas**
protein: /Users/sergei/Development/hyphy-analyses/codon-msa/example.fas_protein.fas
rna: /Users/sergei/Development/hyphy-analyses/codon-msa/example.fas_nuc.fas
[Data QC] Will write unaligned protein sequences for MSA to **/Users/sergei/Development/hyphy-analyses/codon-msa/example.fas_protein.fas**, and the corresponding nucleotide sequences to **/Users/sergei/Development/hyphy-analyses/codon-msa/example.fas_nuc.fas**
[Data QC] Found 1 unique sequences that were in frame
[Data QC] Correcting frame-shifts in the remaining reads
[Data QC] Checking for frame-preserving indels in other reads
[Next steps] Please run **/Users/sergei/Development/hyphy-analyses/codon-msa/example.fas_protein.fas** through an MSA program, and then run post-msa.bf on the output and **/Users/sergei/Development/hyphy-analyses/codon-msa/example.fas_nuc.fas** to recover the nucleotide MSA

[3]. muscle -in example.fas_protein.fas -out example.fas_protein.msa

[4]. hyphy post-msa.bf --protein-msa example.fas_protein.msa --nucleotide-sequences example.fas_nuc.fas --output example.msa

compress: Yes
code: Universal

Analysis Description
--------------------
 Map a protein MSA back onto nucleotide sequences 

- __Requirements__: A protein MSA and the corresponding nucleotide alignment

- __Citation__: TBD

- __Written by__: Sergei L Kosakovsky Pond

- __Contact Information__: spond@temple.edu

- __Analysis Version__: 0.01

Load the protein MSA
protein-msa: example.fas_protein.msa
Load the unaligned in-frame sequences
nucleotide-sequences: example.fas_nuc.fas
output: example.msa
[UNIQUE SEQUENCES] Retained 27 unique  sequences

Or [to not compress duplicate sequences]

[4] hyphy post-msa.bf --protein-msa example.fas_protein.msa --nucleotide-sequences example.fas_nuc.fas --output example-all.msa --compress No