[EMBOSS] water problems

[Gila Lithwick]

Hello,

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 
default.

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.

Thank you,
Gila.