Hi, I'm checking to see if you guys may be able to help me with an algorithm for finding patterns. I have around 2000 short sequences (of length 9) that are aligned. I want to be able to extract all common patterns on the same positions and report the number of occurrences. For example in the following: 1.ACGCATTCA, 2.ACTGGATAC, 3.TCAGCCATC I would like the following output (where a full stop represents any character): (AC....T..) 2 occurrences -pattern between sequence 1 and 2. (.C.G....C) 2 occurrences -pattern between sequence 2 and 3. (.C.......) 2 occurrences -pattern between sequence 1 and 3. As you can see, the way that I am planning on doing this now requires sum(n-1...1) comparisons. Is there a more efficient way of doing this with less comparisons? If there are any existing algorithms that you think may be better suited, please let me know. Thanks

In reply to pattern finding algorithm by kdt2006

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