ConSurfDB vs. ConSurf: Difference between revisions
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===Too Many Sequences=== | ===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. | 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. Start a new job, with the only difference being the database searched. | ||
===Using Your Results=== | ===Using Your Results=== | ||