[BiO BB] Emboss help

govind mk mkgovindis at yahoo.com
Tue Feb 26 22:07:06 EST 2002

Hello users,

This email is from the person who has written the program Showalign ...

The uppercase consensus symbols is meant to indicate that the consensus is strong and lowercase indicates that it is weak. In practice, I don't really like this feature and genarally turn it off.

The cutoff for setting  the case of the consensus is set by the
qualifier '-setcase'.
If the score of the matches is above this value, then the symbol is in
uppercase, iot the score is below the -setcase value then the symbol is in lowercase.

To put all of the consensus symbols into uppercase or lowercase, make
-setcase very low (-100000 ?) or very large (100000 ?)

selvi subramanian <selonline at hotmail.com> wrote: 
well i believe the conservative replacements are denoted by x and the non 
conservative as X, govind!!!



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