I have dynein inhibitors, and want to prove that they inhibit the dyneins of Leishmania (my model organism of interest). I would like to perform an amino acid conservation analysis where I can show that leishmanial dynein sequences are conserved/similar to dyneins of other organisms (say Chlamydomonas).
What would be the correct software to use for the same which can provide me with a conservation score or something similar?
Use leishmanial dynein sequences and the sequences of dyneins of other organisms and performed multiple sequence alignment to check the sequence conservation. You can use MUSCLE, CLUSTALW, T-COFFEE for alignment and you can visualize the multiple sequence alignment using JALVIEW.
Hi Rajesh. Thanks for your answer. I am aware of CLUSTALW as an MSA tool. However, will the alignment provide me with identity scores? Or basically I have to check each and every amino acid manually for conservation?
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