x-rated acedb

Jean Thierry-Mieg mieg at ncbi.nlm.nih.gov
Wed Sep 27 03:58:38 EST 2000


>So whilst 'X' may not be a standart IUPAC code, it is the case that some
>researchers will use 'X'...maybe acedb could run a simple check when
>sequences are loaded and not accept sequences with any non-standard
>code...or at least inform the curator when something non-standard is 
read
>in. 
> 
> 
>> 'X' is not an IUPAC
>> nucleotide ambiguity code (I think it is the protein ambiguity code).
> 
>

acedb> parse
// Type in your data in .ace format, then CTRL-D to finish
DNA toto
atgc
axgc

// 1 objects read with 0 errors
// 1 Active Objects
acedb> find dna toto

// Found 1 objects in this class
// 1 Active Objects
acedb> show

DNA : "toto"
         atgca-gc

so x is treated as a place holder
which is probably what yuo want
considering that some biologists may use it


i apologize for my letter of 2 days ago, i  guess
i was in a bad mood

jean








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