Hello!

I am very new to biopython and I am trying to accomplish what I think is a simple task: I would like to remove sequences from a protein alignment that do not contain a particular residue at a specified position. I would like to be able to input a protein alignment in fasta format and then output a new alignment where all the sequences that do not meet my criteria are removed

For example: My input protein alignment contains sequences that have a mixture of residues at position 137. I would like to output a new alignment that contains only sequences that have either an arginine or a valine at position 137.

Just a bit of additional clarification: I am sequencing an amplicon of a functional gene and generating protein sequence alignments using RDP's fungene pipeline. I want to further screen the alignment by eliminating any sequences that do not contain a selection of conserved residues at various positions.

Thank you very much for your time.

-J
    python script.py <file.fasta>

 - read in the sequence `from Bio import SeqIO` and store them in a dictionary. Print Sequences in a file.
 - align the sequence file with tool of your choice.
 - read in the alignment using from Bio import AlignIO
 - iterate through the alignment, and check the residues you are interested.
 - make a list of the ones to kept or thrown. Delete your alignment file.
 - Print the remaining sequences and re-do alignment.

Hope I haven't confused it.