Determine whether peptide sequences are novels with respect to seed peptides
0
0
Entering edit mode
3.2 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.

alignment sequence • 581 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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?

ADD REPLY

Login before adding your answer.

Traffic: 1639 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6