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Peptide

Ed Griffiths edgrif at sanger.ac.uk
Wed Jan 23 04:24:04 EST 2002


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 protein
> 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, the
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 length
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 is
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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