Difference between revisions of "User:Scmohr/Specialized Doc Score"

(New page: =Additional (or Modified) Documentation Required for Specific Categories of Simple Parts= (Relative to All Parts List of 8/20/07) Scott C. Mohr (8/21/07) Protein coding sequences (CDS...)
 
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=Additional (or Modified) Documentation Required for Specific  Categories
+
=Additional (or Modified) Documentation for Specific  Categories of Basic Parts=
−
of Simple Parts=
+
 
(Relative to All Parts List of 8/20/07)
 
(Relative to All Parts List of 8/20/07)
  
 
Scott C. Mohr
 
Scott C. Mohr
−
(8/21/07)
+
(8/21/07; updated 7/2/08)
  
−
Protein coding sequences (CDS’s) / Repressors and Activators
+
==Protein coding sequences (CDS’s) / Enzymes (CDS-E)==
  
 
ADD:
 
ADD:
  
−
Repressor?  ______ (yes/no) Activator______ (yes/no)
+
* E-1 Enzyme Commission (EC) number (if assigned) <SPAN style= 'color:red'>'''(1)'''</span>
  
−
N.B. Both choices are necessary since some proteins are repressors under some circumstances and activators under other circumstances.
+
* E-2 Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) <SPAN style= 'color:blue'>'''(1)'''</span>
  
−
Regulatory ligands/effects: _____________________ (list in a box?)
+
==Protein coding sequences (CDS’s) / Repressors and Activators (CDS-RA)==
  
−
OMIT:
+
ADD:
−
E.C. number
+
 
−
+
* RA-1 Repressor?  ______ (yes/no). Activator?______ (yes/no). Both?______ (yes/no) <SPAN style= 'color:red'>'''(1)'''</span>
−
Protein coding sequences (CDS’s) / Reporters
+
 
 +
''N.B.,'' Some proteins are repressors under some circumstances and activators under other circumstances.
 +
 
 +
* RA-2 Regulatory ligands/effectors: _____________________ (list in a box?) <SPAN style= 'color:red'>'''(1)'''</span>
 +
 
 +
==Protein coding sequences (CDS’s) / Reporters (CDS-R)==
  
 
ADD:
 
ADD:
  
−
Fluorescent ? yes/no b. Luminescent ? yes/no c. Other ? __________
+
*R-1 Fluorescent? ______ (yes/no). Luminescent? ______(yes/no). c. Other? __________ <SPAN style= 'color:red'>'''(1)'''</span>
  
−
Spectroscopic data: (a) absorption max. ______ m
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*R-2 Spectroscopic data: <SPAN style= 'color:blue'>'''(2)'''</span>
−
(b) emission max. ______ m
+
−
(c) luminescent max. ______ m
+
−
(d) other notable spectroscopic features:  _____________
+
−
_________________________________________________
+
−
    _________________________________________________
+
−
Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS!
+
  
−
OMIT:
+
# absorption max. ______ nm 
−
E.C. number
+
# emission max. ______ nm
 +
# luminescent max. ______ nm
 +
# other notable spectroscopic features:  _____________
 +
 
 +
 
 +
________________________________________________________
 +
 
 +
Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS!  <SPAN style= 'color:red'>'''(1)'''</span>
 +
 
 +
E.C. number (if applicable) <SPAN style= 'color:blue'>'''(1)'''</span>
  
−
Protein coding sequences (CDS’s) / Uncategorized
+
==Protein coding sequences (CDS’s) / Uncategorized (CDS-U)==
  
 
ADD:
 
ADD:
 
nothing
 
nothing
 
OMIT:
 
OMIT:
−
E.C. number
+
nothing
−
Protein coding sequences (CDS’s) / Fusion proteins (new category)
+
 
 +
==Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (CDS-F, new category)==
  
 
ADD:
 
ADD:
  
−
Method used to fuse the two components.
+
Method used to fuse the two components. <SPAN style= 'color:red'>'''(2)'''</span>
−
Feature annotation of the linker spanning the two fused segments
+
 
−
Sources of both sequences.
+
Feature annotation of the linker spanning the two fused segments <SPAN style= 'color:red'>'''(1)'''</span>
 +
 
 +
Sources of ''both'' sequences. <SPAN style= 'color:red'>'''(3 + 3 = 6)'''</span>  [Note the high point value!]
  
 
OMIT:
 
OMIT:
 +
 
E.C. number(s) – if inappropriate
 
E.C. number(s) – if inappropriate
  
−
Ribosome binding sSites (RBS’s
+
==Ribosome binding Sites (RBS’s)==
  
 
ADD:
 
ADD:
 
nothing
 
nothing
 
OMIT:
 
OMIT:
−
E.C. number
+
Nothing
−
SwissProt number
+
  
−
Terminators
+
==Terminators==
  
 
ADD:
 
ADD:
−
nothing
+
nothing (best mFold structure?)
 
OMIT:
 
OMIT:
−
E.C. number
+
nothing
−
SwissProt number
+
  
−
Promoters (suggested renaming of “Regulatory regions”)
+
==Promoters (suggested renaming of “Regulatory regions”)==
  
 
ADD:
 
ADD:
 
•In the part “long description,” INDICATE SPECIFICALLY IF THIS IS A COMPOSITE PART (i.e. whether or not it encodes a repressor/activator binding site, and if so, the identity of the repressor/activator and co-repressor/inducer.)
 
•In the part “long description,” INDICATE SPECIFICALLY IF THIS IS A COMPOSITE PART (i.e. whether or not it encodes a repressor/activator binding site, and if so, the identity of the repressor/activator and co-repressor/inducer.)
−
•Under dependencies, be sure to include chassis type, growth conditions and any other key factors that relate to the promoter function.
+
<SPAN style= 'color:red'>'''(2)'''</span>
 +
 
 +
•Under dependencies, be sure to include chassis type, growth conditions and any other key factors that relate to the promoter function. <SPAN style= 'color:red'>'''(2)'''</span>
 +
 
 
OMIT:
 
OMIT:
−
E.C. number
+
nothing
−
SwissProt number
+
 
   
 
   
−
RNA (suggestions needed)
+
==RNA==
 +
(suggestions needed!)
  
 
ADD:
 
ADD:
 
nothing
 
nothing
 
OMIT:
 
OMIT:
−
E.C. number
+
nothing
−
SwissProt number
+
  
−
DNA (suggestions needed)
+
==DNA==
 +
(suggestions needed!)
  
 
ADD:
 
ADD:
 
nothing
 
nothing
 
OMIT:
 
OMIT:
−
E.C. number
+
nothing
−
SwissProt number
+
  
−
Conjugation (suggestions needed)
+
==Conjugation==
 +
(suggestions needed!)
  
 
ADD:
 
ADD:
 
nothing
 
nothing
 
OMIT:
 
OMIT:
−
E.C. number
+
nothing
−
SwissProt number
+
 
 +
SCM (7/2/08)

Latest revision as of 19:00, 2 July 2008

Additional (or Modified) Documentation for Specific Categories of Basic Parts

(Relative to All Parts List of 8/20/07)

Scott C. Mohr (8/21/07; updated 7/2/08)

Protein coding sequences (CDS’s) / Enzymes (CDS-E)

ADD:

* E-1 Enzyme Commission (EC) number (if assigned) (1)

* E-2 Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) (1)

Protein coding sequences (CDS’s) / Repressors and Activators (CDS-RA)

ADD:

* RA-1 Repressor? ______ (yes/no). Activator?______ (yes/no). Both?______ (yes/no) (1)

N.B., Some proteins are repressors under some circumstances and activators under other circumstances.

* RA-2 Regulatory ligands/effectors: _____________________ (list in a box?) (1)

Protein coding sequences (CDS’s) / Reporters (CDS-R)

ADD:

*R-1 Fluorescent? ______ (yes/no). Luminescent? ______(yes/no). c. Other? __________ (1)

*R-2 Spectroscopic data: (2)

  1. absorption max. ______ nm
  2. emission max. ______ nm
  3. luminescent max. ______ nm
  4. other notable spectroscopic features: _____________


________________________________________________________

Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS! (1)

E.C. number (if applicable) (1)

Protein coding sequences (CDS’s) / Uncategorized (CDS-U)

ADD: nothing OMIT: nothing

Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (CDS-F, new category)

ADD:

Method used to fuse the two components. (2)

Feature annotation of the linker spanning the two fused segments (1)

Sources of both sequences. (3 + 3 = 6) [Note the high point value!]

OMIT:

E.C. number(s) – if inappropriate

Ribosome binding Sites (RBS’s)

ADD: nothing OMIT: Nothing

Terminators

ADD: nothing (best mFold structure?) OMIT: nothing

Promoters (suggested renaming of “Regulatory regions”)

ADD: •In the part “long description,” INDICATE SPECIFICALLY IF THIS IS A COMPOSITE PART (i.e. whether or not it encodes a repressor/activator binding site, and if so, the identity of the repressor/activator and co-repressor/inducer.) (2)

•Under dependencies, be sure to include chassis type, growth conditions and any other key factors that relate to the promoter function. (2)

OMIT: nothing

RNA

(suggestions needed!)

ADD: nothing OMIT: nothing

DNA

(suggestions needed!)

ADD: nothing OMIT: nothing

Conjugation

(suggestions needed!)

ADD: nothing OMIT: nothing

SCM (7/2/08)