+----[ BHurwitz@twt.com <BHurwitz@twt.com> (25.Jun.2004 15:56): | | Sequences are appearing to have the same expect value | although the matches in the hsp are very different. The question you should be asking is why the alignments below have the same score. If they have the same score, they'll have the same E value, since the E value is (by definition) the number of alignments with a score >= S (24.3 bits in this case) that you expect to occur by chance. Have you indexed the databases using a 2.2.9 formatdb? Perhaps you're using databases indexed with an older formatdb?. I've also seen strange results myself in the past, and the problem was that somehow the indices created by older versions of formatdb would not be properly read by the newer blast executables. Hope this helps, Fernan | From blast: | | > 5846704 | Length = 177 | | Score = 24.3 bits (12), Expect = 0.16 | Identities = 18/20 (90%) | Strand = Plus / Minus | | Query: 13 ctccagacattgggcgggtt 32 | |||||| ||||| ||||||| | Sbjct: 127 ctccaggcattgagcgggtt 108 | | | > 5714596 | Length = 9401 | | Score = 24.3 bits (12), Expect = 0.16 | Identities = 8/20 (40%) | Strand = Plus / Minus | | | Query: 13 ctccagacattgggcgggtt 32 | | ||| | ||| | Sbjct: 202 tccaagaaaggacccggtcg 183 | | -Bonnie | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan