When we are in the step of aligning virulent factors against human proteom to exclude those proteins with > 35% homology what is the output that we have to use for the next step of predicting transmembrane helices and molecular weight for chosen proteins?
Hi Ahmed,
I'm not sure I understand your question correctly, but I assume you have an output file somewhere where sequence redundancy has been removed to 35% sequence identity or whatever?
Thus you give a (protein) sequence .fasta file to the transmembrane helix predictor of the proteins contained within. As for Molecular weight, I think there are some web servers which will calculate molecular weight of a protein based on its sequence, so use that fast file there also.
Hope that helps
Hi Mr David thank you so much for your answer, I really appreciate your help. My question is that do we use the non-homologus protein sequence aligned related to homosapiens, or do we use the original sequence submitted e.g. (virulent factors) for further steps. And if we use the later (the non-homologus protein sequence related to my specie of interest) then from where can we obtain the output fasta sequence on the blast p platform.
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