[Bioperl-l] Specification of features tables (on translation mixed with replace qualifiers)

[Carnë Draug]

HI

I have been reading the specifications for feature tables by
DDBJ/EMBL/GenBank so I can get all my plasmids saved properly but I
don't know how to deal with a specific situation. I have many plasmids
that I mutated by site-directed mutagenesis. It seems that in this
cases, I should keep the sequence of the entry intact (compared to the
original), and simply use the misc_difference feature with a replace
tag/quantifier (from the specifications document: "the misc_difference
feature key should be used to describe variability that arises as a
result of genetic manipulation (e.g. site directed mutagenesis)".

What I wonder is if the translation tag in the CDS feature should be
of the mutated sequence (checking for the replace tag), or the
translation of the actual entry sequence? The specification does not
specify such, it defines it as: "automatically generated one-letter
abbreviated amino acid sequence derived from either the universal
genetic code or the table as specified in /transl_table and as
determined by exceptions in the /transl_except and /codon qualifiers".

By the way, I was testing this with bioperl and Bio::SeqIO and here
some things I found, some of them may be bugs:
  * when using the translate method, it translates the sequence of the
entry ignoring replace tags
  * when saving the entry for a file, it does not check if the
/translate value of the CDS feature is correct

Also, is there a module that I can use to validate a sequence file?

Thanks in advance,
Carnë