I want to generate a multiple sequence alignment that retains the annotations I made on a list of protein sequences (eg. Stockholm file format). Is there a way to do this? Maybe with Biopython or Biostrings?
In the end, all I want is a MSA with the same annotations as the orignal sequences, so any way that I can add annotations to a MSA without annotations will work as well.
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DNAlias •
1 answer
Muscle can do this. If you save your alignment in aligned FASTa (.afa) format, which is default, all sequence headers will be preserved. Assuming your starting file is protein.fas:
muscle -in protein.fas -out protein.afa
After that the alignment can be converted to Stockholm format using HMMer's esl-reformat utility:
esl-reformat stockholm protein.afa > protein.sto
The old version of esl-reformat is sreformat, and it can convert GenBank to FASTa.
sreformat fasta genome.gbk > genome.fas
You will need to go to older HMMer version, I think v2.3, to find this program.
If this doesn't work, Google is your friend. There should be plenty of programs or scripts to convert GenBank to FASTa.
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