Dear Friends, I have punch of proteins in a particular family from different species for eg. Species 1: 240, Species: 100 and Species3: 300. I want to do comparative analysis between species. Before that I must remove reduntant or overlapping proteins with in the species. I have already selected the proteins based on HMMER from the repective species. I need to screen more to get the actual number of proteins present in the each species of particular family. For that I am using BLAST+ to blast each species itself and remove the sequences having more than 70% identity by considering the sequences have more than 70% as one. So that I keep one sequence and remove all others in the one group. Like this I can trim protein seqeunces. For eg., Species 1: 240 into some around 70 or 80 depends on its similarities. I am not sure whether this idea is correct or not ...? If the idea is correct, is it possible to fix the percentage identity in the blast+ using -perc_identity 70. I have tried it but it shows "Unknown argument: "perc_identity"". Could anyone suggest me to get ride of similar or repeated sequence in the family.
Question: Can we fix the identity percentage in blast+ stand alone software ?
2.8 years ago by
S. Prabhakaran • 0
S. Prabhakaran • 0 wrote:
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