Hi all,

I have a list of 60 different insertion and deletion mutant proteins, and I’d like to perform a multiple sequence alignment comparing each mutant with the wild-type sequence. The Needleman-Wunsch global alignment tool on NCBI works well, but it only allows aligning a single mutant with the wild type at a time.

Do you know of a way to perform this global alignment on multiple proteins from the mutant list in one go?

Note that standard local alignment tools don’t work properly, as they tend to mismatch the insertion or deletion mutations (stretches of 5 to 10 amino acids) with the wild-type sequence.

Thanks

If you don't want to program, you can use exonerate or needle from the EMBOSS suite.

You can use the bio with the align tool. Install with pip install bio then

bio align query.fa target.fa

You can put all the targets in the target.fa, and it will generate alignments of the query to each target.

The tools support local, global, and semi-global alignments; you can pass scoring matrices. Works seamlessly for nucleotide and protein alignments.

It does have limitations since it relies on an optimal alignment algorithm from BioPython—realistically, it tops out at around 30K bases. I would not use it for sequences longer than that.

Docs: https://www.bioinfo.help/bio-align.html