mapping thousands of random k-mer peptides against one protein sequence

Question

[vinni]

Dear BioStars community, I am trying to map thousands of 12-mer peptide sequences to a single protein and check the efficacy of each alignment. I've already tested Relic Match and GuiTope programs, which both work only on windows and produce different errors when using large input files with peptide sequences. Any advices, ideas or software recommendations will be much appreciated. Thank you in advance!

Answer 1

[dariober]

What about blast? It shouldn't take long for a few thousands queries against one protein.

[vinni]

I am actually working with hundreds of thousands peptide mimotopes. The goal is to map them and then to calculate the 'best' residue score for each protein site using some structural similarity parameter. blastp alignment will take forever. Thanks anyway!

Answer 2

[dariober]

Option 2: What about vmatch? It's free but you need to ask the authors to send you the license key.