A collection of useful scripts
The scripts in this repo should run on any UNIX system (Linux or MacOS).
The scripts in this repo use the following command line tools:
mafft- a popular sequence alignment toolsmof- a sequence manipulation utility available on PyPi
The scripts extractHA1.sh and extractHA1-CDS.sh extract the HA1 amino acid
or coding sequence, respectively, from an HA gene. Currently it these scripts
will work automatically for H1 or H3 segments.
The regions are extracted by first aligning the input DNA sequence and then finding the locations of each HA1 match on the gapped sequences. The interval that is most common is used to take substrings from the aligned sequences. This approach is very robust against bad or unusual sequences. It will work so long as more sequences match the given pattern then match any other irregular pattern.
For H1, the expected HA1 regular expression pattern is DT[LI]C.*QSR. For H3,
it is QKL.*QTR.
For an input file myseq.fasta, the files myseq.fasta.aln (the multiple
sequence alignment) and myseq.fasta_HA1.faa (for extactHA1.sh) or
myseq.fasta_HA1.fna (for extractHA1-CDS.sh) will be created.
The script 'antigenic_motif.py' extracts the antigenic sites from aligned H1 nucleotide data. It will convert the nucleotide data into amino acid sequence and will extract the relevant sites. Sites are extracted based on H1 numbering.
List of sites:
Ca-2 140 143 145 224 225
Cb 78 79 80 81 82 83 122
Sa 128 129 158 160 162 163 165 167
Sb 156 159 192 193 196 198
For input file, align your H1 nucleotide data.
Run it as, python antigenic_motif.py aligned_input.fasta
Output will be written to aligned_input.fasta-AB-AntigenicSites.txt```