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Understanding CAS Registry BLAST Results

These are common questions and answers to help you understand the search process and your search results. See View Your Search Result for an explanation of the contents of a sequence result set and search parameters.

Q: Why does a string of "Xs" (or "Ns") unexpectedly appear in my query sequence after the query is run?

A: This is the result of filtering your query for low-complexity sequences.

Filtering masks off segments of the query sequence that have low compositional complexity. Filtering can eliminate statistically significant but biologically uninteresting results from the BLAST® output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences. Filtering is only applied to the query sequence (or its translation products), not to database sequences.

The filters work by substituting the letter "N" (e.g., "NNNNNNNNNNNNN") in low-complexity nucleotide sequences or the letter "X" (e.g., "XXXXXXXXX") in low-complexity protein sequences.

To remove low-complexity filtering from a query:

  1. Re-run your query and go to the Settings window for your program.
  2. Under Basic Options, deselect Low Complexity Filtering.

Q: What would cause me to receive zero results?

A: There are several reasons that a CAS Registry BLAST search might not retrieve any hits. Try the following approaches, alone or in combination:

Q: The sequence name in my BLAST report reads "INDEX NAME NOT YET ASSIGNED." What does this mean and how does it affect CAS Registry BLAST Alert reports?

A: To ensure that searchers have access to the newest sequences, sequences become available in the database before a name is assigned. When a name is assigned (the interval is usually several weeks), your BLAST and Alerts reports will be updated with assigned names for the first 600 "not yet assigned" sequences.

Restriction: Rarely, an assigned sequence name will change. In such instances, the name is not updated and the first assigned name is retained.


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