Entering edit mode
5.7 years ago
abeltran
•
0
Hello, everyone,
Currently, I have designed peptide sequences, and now I want to compare those sequences with the seed sequences. My question is related to whether it is correct to perform global pairwise alignment sequences and to calculate the identity percentage to determine if the sequences are really novels. My second question is about how you can plotting this result to show the differences between the sequences.
Can you comment on the lengths of peptides and the seed sequences? You could look at doing dot plots to visualize the similarities if the lengths are comparable.
Sure, the peptide length have a length between 7 and 48 residues, also the number of the peptides is aprox. 2k for the seed peptides and 1k for the design peptides.
Pardon the additional questions but I am trying to get relevant information so someone could step in with a suggestion.
With a range of between 7 and 48 AA there is no point in doing global alignments. Do you expect the core sequence to be present ungapped? e.g. if the 7 AA is contained in 48 would there be a single ungapped copy or multiple copies? Is the dataset already non-redundant i.e. have you removed duplicates of equal length?