AMP_alignment_process

A workflow and toolkit of perl scripts to manipulate multiple sequence alignments

Usage

1. In a directory that contains nucleotide sequence fasta files, run

perl scriptPath/run_AMP_alignment_process.pl –id directoryPath(default: .)

• Renames file names beginning with “Hxxx” to “Vxxx” and renames sequence names within each the file with the standard nomenclature
• Merges sequence files for the same sample ID, based on file names
  • Creates subdirectory “GP/REN” to store merged sequence files and files produced by the following steps
• Collapses identical sequences into unique sequences, adds the number of sequences that were collapsed to the sequence name
• Muscle aligns collapsed sequences

2. Manually inspect/edit refined alignments

3. In the directory that contains both the inspected alignments and a reference alignment, run

perl scriptPath/run_ref_sample_profile_alignment.pl –id directoryPath(default: .) 
–ref referenceFileName

• Merges reference alignment to participant sequence alignment by profile alignment

4. Manually inspect/edit reference containing alignments

5. In the directory that contains the inspected reference-included alignments, run

perl scriptPath/run_extraction_translation.pl –id directoryPath(default: .) 
–sp startPositionOfGagOrRevInHXB2

• Extracts gene regions (Gag, Pol, Prot for GP; Rev, Vpu, Env, Nef for REN) in alignment based on the start positions in HXB2 within alignment
  • Creates subdirectories of gene regions to store extracted alignments and files produced by following steps
• Translates extracted nucleotide sequence alignment a corresponding amino acid sequence alignment

6. Manually inspect/edit translated amino acid alignment and adjust corresponding nucleotide alignment as needed

7. In the directory that contains alignments needed to be uncollapsed and the corresponding .name files, run

perl scriptPath/uncollapse_seqs.pl inputFile nameFile

• Uncollapses alignment into full alignment of individual sequences with sequence names