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Peptide <3C4D3AA1.6B2BCFD5@sanger.ac.uk>

Qunfeng Dong qfdong at iastate.edu
Thu Jan 24 06:09:41 EST 2002


Thanks, Ed! It seems that line breaker character '\n' was part of
reasons that caussd trouble. After I delete all line breaker in peptide
seq, I can load the seq into AceDB (BTW, AceDB4.9).

Qunfeng


>Qunfeng Dong,
>
>> Somebody must have asked this question before. I am sorry I have to ask this
>> because Surprisingly I can't find any document describing how to load protei
n
>> sequence into AceDB. Isn't the usage of Peptide the same as DNA? Please help
!
>
>Yes, I think it is, it seems to work for me. But.....some points to note...
>
>> ps.what's wrong with the following simple ace file?
>
>> When I tried to load this file, xace hangs at
>> Item: 2 Q08062
>> Line: 4 (49%)
>> Pased: 2
>> OK:    2
>> Errors: 0
>
>Sorry, this is a bug in acedb to do with the way the file IO package works, th
e
>last length it reports is the length where the last object _starts_, when the
>code runs out of stuff to read it does an implicit close and we lose the lengt
h
>of stuff parsed so far. If you have a long ace file you don't notice because
>rounding means that the % always looks like the whole file was parsed...sigh.
>(Don't you just hate implicit closes)
>
>The effect is that when you parse a short ace file it looks like it wasn't all
>parsed correctly. In the below example when I look in the database, the data i
s
>all there.
>
>One point to note...in the below why do put the length as "40" when it is "82"
 ?
>
>> ------------------------------------------------------
>> Protein : Q08062
>> Title "Malate dehydrogenase, cytoplasmic."
>> Peptide Q08062 40
>> 
>> Peptide : Q08062
>> MATQTAVTATTVPQGSPSVTGSASQGGILNSARQFFSLAAPKVEKDKEFSFRFLTSP
>> LRSKPAATVNADNFYMYACGSINMP
>> ------------------------------------------------------
>
>cheers Ed
>
>-- 
> ------------------------------------------------------------------------
>| Ed Griffiths, Acedb development, Informatics Group,                    |
>|        Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,  |
>|               Hinxton, Cambridge CB10 1SA, UK                          |
>|                                                                        |
>| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
> ------------------------------------------------------------------------
>

       
      
      
       





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