Re: [Gusdev-gusdev] New Table View? TransMembrane AASeqFeature

[Ed R. <ero...@ug...>]

The long and short of it is at the end of the message.  
A table that stores the values in short output is really all I
need (Despite my dislike for storing string-coded arrays in
row attributes, normalizing the long ourput to two tables is a
bit excessive).  I assume this is all in the table Mike
mentioned:  AASequenceID, Length, NumberAAsPredictedTM,
NumberPredictedTMFirst60, TotalNumberTMRegions, Topology.

-ed


Long Output:
# COX2_BACSU Length: 278
# COX2_BACSU Number of predicted TMHs:  3
# COX2_BACSU Exp number of AAs in TMHs: 68.6888999999999
# COX2_BACSU Exp number, first 60 AAs:  39.8875
# COX2_BACSU Total prob of N-in:        0.99950
# COX2_BACSU POSSIBLE N-term signal sequence
COX2_BACSU        TMHMM2.0        inside       1     6
COX2_BACSU        TMHMM2.0        TMhelix      7    29
COX2_BACSU        TMHMM2.0        outside     30    43
COX2_BACSU        TMHMM2.0        TMhelix     44    66
COX2_BACSU        TMHMM2.0        inside      67    86
COX2_BACSU        TMHMM2.0        TMhelix     87   109
COX2_BACSU        TMHMM2.0        outside    110   278 

Short Output:
COX2_BACSU
len=278
ExpAA=68.69
First60=39.89
PredHel=3
Topology=i7-29o44-66i87-109o 


---- Original message ----
>Date: Tue, 15 Feb 2005 10:37:16 -0500
>From: Steve Fischer <sfi...@pc...>  
>Subject: Re: [Gusdev-gusdev] New Table View?  TransMembrane
AASeqFeature  
>To: Ed Robinson <ero...@ug...>
>Cc: gus...@li...
>
>ed-
>
>can you provide a more detailed proposal?
>
>steve
>
>Ed Robinson wrote:
>
>>I need to store more information for TransMembrane domains
>>than PredictedAAFeature presently allows.  Can we create a new
>>view on AAFeatureImp or can we expand the number of attributes
>>in PredictedAAFeature?
>>
>>-ed
>>
>>-----------------
>>Ed Robinson
>>Center for Tropical and Emerging Global Diseases
>>University of Georgia, Athens, GA 30602
>>ero...@ug.../(706)542.1447/254.8883
>>
>>
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-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883