How can I see low-similarity matches whe...

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How can I see low-similarity matches when there are many strong hits to my query sequence?

Often, when the query is a member of a large sequence family, the summary hit list and the alignments returned only contain very high scoring hits. To look at low-similarity matches, you must increase the maximum number of results returned. On the BLAST Web pages, often it is sufficient to increase the size of the summary hit list and the number of alignments shown using the menus on the Advanced pages. However, it is possible to increase the lists even further using the Other Advanced Options box on the Advanced BLAST pages. For BLAST 2.0, "-v 2000", for example, will increase the number of descriptions returned in the summary hit list to 2000. The option "-b 2000" will similarly increase the number of alignments returned.

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Other Frequently Asked Questions

• Can I use BLAST to compare to two or more sequences in a multiple sequence alignment?
• How can I limit my BLAST search based on Organism?
• How can I search a batch of sequences with BLAST?
• After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?
• Why does my search timeout on the BLAST servers?
• What is the Expect (E) value?
• I have heard that I will be penalized if I send a large number of sequences to the servers?
• Why do I get the message "ERROR: Blast: No valid letters to be indexed"?
• Causes for "No significant similarity found"
• How can I limit my search to a "subset" of database sequences?
• More...