Can someone point us towards analysis software that is able to identify similar short protein sequences within a protein database through use of a set of comparisons (e.g., similar charged or structural) amino acids) and with a base short protein sequence (say a 10aa sequence)?
Rob Keller
Dear Vincent Bond
Two approaches cross my mind:
BLAST see for example https://www.ebi.ac.uk/ipd/mhc/blast/#:~:text=The%20BLAST%20engine%20is%20designed,acids%20(proteins%2Fblastp). (minimum length is 6 AA)
Or
Heliquest https://heliquest.ipmc.cnrs.fr (unfortunately what you are aiming for only works with a length of 18 AA sequences)
Best regards.
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