ConSurfDB vs. ConSurf: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
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If your results have more than a few amino acids with insufficient data (<span style="color: yellow; background-color: black;"><b> yellow color </b></span>), you need more sequences. Try repeating the procedure above with one change. Under "Choose parameters to homolog search algorithm", change the ''Proteins Database'' to UniProt or NR (larger databases than the default Uniref90). | If your results have more than a few amino acids with insufficient data (<span style="color: yellow; background-color: black;"><b> yellow color </b></span>), you need more sequences. Try repeating the procedure above with one change. Under "Choose parameters to homolog search algorithm", change the ''Proteins Database'' to UniProt or NR (larger databases than the default Uniref90). | ||
If the NR database does not give enough sequences, you can use other options to widen the search for sequences, knowing that you will be retrieving sequences less related to the query sequence, likely including proteins with functions differing from that of the query: | |||
* Increase the number of iterations in the search to more than the default of one. Each iteration generates a sequence profile that is used as a query for the next iteration. | |||
* Increase the default E cutoff of 0.0001, for example, to 0.001 or 0.01. | |||
* Increase the "Maximal %ID between sequences" from the default of 95% to perhaps 98%. | |||
===Using Your Results=== | ===Using Your Results=== | ||