[EMBOSS] water problems
gilal at md.huji.ac.il
Wed Dec 3 14:47:51 UTC 2003
I wasn't sure which mailing list this e-mail is more appropriate for, so
I've sent it to both...
I have been using EMBOSS, and noticed the following problems with water:
1) Water does not give a gap extension penalty for the first gap. This
is not how gaps are generally penalized.
For example, the alignment between tttttcccaaaaa and tttttaaaaa is:
seq1 1 tttttcccaaaaa 13
seq2 1 ttttt---aaaaa 10
EMBOSS scores this 39, however the score should be 10*5-3*0.5-10=38.5
Is this correct?
2) Since the default gap extension penalty is so low (0.5), water often
gives very long alignments. A slightly higher gap penalty (for example
1) gives better alignments - maybe it would be better to make this the
3) It would be very useful if there was a way to assess significance of
pairwise alignments, such as the -rand option in gcg. It is possible,
of course, to do each step (shuffling one sequence, aligning, and
calculating the mean and standard deviation) separately. However, for
users that don't know how to program, this isn't simple.
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