Peptide

Jean Thierry-Mieg mieg at ncbi.nlm.nih.gov
Wed Jan 30 04:20:43 EST 2002


sorry
i do not reproduce the error

acedb> parse
// Type in your data in .ace format, then CTRL-D to finish
Protein : Q08062
Title "Malate dehydrogenase, cytoplasmic."
Peptide Q08062 40

Peptide : Q08062
MATQTAVTATTVPQGSPSVTGSASQGGILNSARQFFSLAAPKVEKDKEFSFRFLTSP
LRSKPAATVNADNFYMYACGSINMP

// 2 objects read with 0 errors
// 2 Active Objects
acedb> 

no problem seen
i can then visualize the data
acedb> find protein  Q08062

// Found 1 objects in this class
// 1 Active Objects
acedb> pep
>Q08062
MATQTAVTATTVPQGSPSVTGSASQGGILNSARQFFSLAAPKVEKDKEFS
FRFLTSPLRSKPAATVNADNFYMYACGSINMP
// 1 object dumped// 1 Active Objects
acedb> 

jean


>To: bionet-software-acedb at net.bio.net
>From: Qunfeng Dong <qfdong at iastate.edu>
>Subject: Peptide 
>Date: Mon, 21 Jan 2002 09:44:07 +0000 (GMT)
>X-Virus-Scanned: by amavisd-milter ( http://amavis.org/ )
>
>
>
>Hi there, 
>
>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!
>
>Qunfeng
>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
>
>with NO error message. Why?
>
>------------------------------------------------------
>Protein : Q08062
>Title "Malate dehydrogenase, cytoplasmic."
>Peptide Q08062 40
>
>Peptide : Q08062
>MATQTAVTATTVPQGSPSVTGSASQGGILNSARQFFSLAAPKVEKDKEFSFRFLTSP
>LRSKPAATVNADNFYMYACGSINMP
>------------------------------------------------------
>
>If I replaced the above seq with 
>makepmrvlvtgaagqigyalvpmiargvmlgadqpvilhmldippaaealngvkmelvd
>
>then I got error message: 
>ERROR - array parse error, near line 0 while parsing "Peptide : Q08062", error 
>was: peptideParse error at line 8 in Q08062 : bad char m(0x6d)
>
>
>Please help!
>
>Qunfeng
>
>
>





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