ConSurfDB vs. ConSurf: Difference between revisions
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#When you are satisfied, scroll to the very bottom of the page and click the ''Submit'' button. | #When you are satisfied, scroll to the very bottom of the page and click the ''Submit'' button. | ||
The results of this "one function" job will usually enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia. | ===Too Many Sequences=== | ||
ConSurf will list up to 2,000 sequences from which to select. In some cases, these sequences are all too similar. Some proteins will retrieve >5,000 sequences with an expectation value (E value) < 1.0e-4 (1.0 times ten to the -4), the default threshold. Then the 2,000th sequence listed may still be very similar to the first sequence listed. This would be true if the 2,000th sequence has a very small E value, such as 1.0e-100. In such a case, you may wish to try searching the Swiss-Prot database, which is much smaller than the default Uniref-90 database. | |||
===Using Your Results=== | |||
The results of this "one protein function" job will usually enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia. | |||
See [[#How to Insert a ConSurf Result Into a Proteopedia Green Link|below]] for instructions on how to make a green-link scene in Proteopedia that shows your single-function ConSurf result. | See [[#How to Insert a ConSurf Result Into a Proteopedia Green Link|below]] for instructions on how to make a green-link scene in Proteopedia that shows your single-function ConSurf result. | ||
