[BiO BB] RE: Some questions of alignment

Evgeny Cheremushkin cheremushkin at ngs.ru
Wed Jun 23 02:12:41 EDT 2004

Hello Yuanji,

Monday, June 21, 2004, 10:47:51 PM, you wrote:

ZY> Dear Evgeny,

ZY> Thank you for your response. I am afraid 'alignment' was not well defined in
ZY> my original post. What I really mean is the possible distribution of
ZY> mismatches (M) along the length (L) of the aligned 2 sequences. Two
ZY> sequences are identical Except for the positions with mismatches. So when M
ZY> = 0, there is only one possible alignment, and when M = 1, there are L
ZY> alignments (the mismatch can be in each of all L positions). I think the
ZY> possible alignments is C(L,M) but not sure.

Yes, it is correct.

ZY> About undetected alignments by blastn. There are several cases. Case 1 is
ZY> that the mismatches are distributed in such a way that no seed alignment (7
ZY> or more nt identical) can be found. Case 2 is that the alignment score is
ZY> reduced by a row of mismatches too much so that blast will not extend the
ZY> alignment to include the mismatches. There might be other cases too. So the
ZY> number of undetected alignments is a function of word size, patterns of
ZY> mismatch distribution,and mismatch punishment and match reward scoring
ZY> scheme.

Please, formalize a problem mathematically.

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Best regards,
 Evgeny                            mailto:cheremushkin at ngs.ru

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