ConSurfDB vs. ConSurf: Difference between revisions
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#Look at the names of the proteins in the list that has checkboxes, under the header "Sequences producing significant alignments:". Find the first case where the function of the protein is not the same as the protein of interest. Usually you will want to exclude sequences for proteins of different functions. | #Look at the names of the proteins in the list that has checkboxes, under the header "Sequences producing significant alignments:". Find the first case where the function of the protein is not the same as the protein of interest. Usually you will want to exclude sequences for proteins of different functions. | ||
#Just below the large red line <font color="red">Please choose which sequences you want to use for ConSurf calculation</font> is a form. Put the number of the last sequence having the same function as the protein of interest in the box "Select the first [ .... ] sequences". Then click on the "Update selection" button. | #Just below the large red line <font color="red">Please choose which sequences you want to use for ConSurf calculation</font> is a form. Put the number of the last sequence having the same function as the protein of interest in the box "Select the first [ .... ] sequences". Then click on the "Update selection" button. | ||
## ConSurf will not accept >500 sequences. 200-250 sequences are plenty. More simply load the server unnecessarily. If the number of the last sequence having the same function as the query protein is higher than 250, use the radio buttons labeled "only every 2nd, 3rd, ..." to reduce the total number of sequences selected. | ## ConSurf will not accept >500 sequences. 200-250 sequences are plenty. More simply load the server unnecessarily. If the number of the last sequence having the same function as the query protein is higher than 250, use the radio buttons labeled "only every 2nd, 3rd, ..." to reduce the total number of sequences selected while sampling the full diversity of the desired sequences. | ||
##The form is confusingly labeled. If you check an "only every" number, then you will need to divide the number in the slot labeled "Select the first" by the "only every" number you selected. For example, if the first 472 sequences have the same function as the query protein, check "only every 2nd" and enter 236 (namely, 472/2) in the "Select the first" slot. | ##The form is confusingly labeled. If you check an "only every" number, then you will need to divide the number in the slot labeled "Select the first" by the "only every" number you selected. For example, if the first 472 sequences have the same function as the query protein, check "only every 2nd" and enter 236 (namely, 472/2) in the "Select the first" slot. | ||
#Examine the list of sequences to make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.) | #Examine the list of sequences to make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.) | ||
