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

(→‎Protein coding sequences (CDS’s) / Reporters)
(→‎Conjugation)
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
=Additional (or Modified) Documentation Required for Specific  Categories of Simple Parts=
+
=Additional (or Modified) Documentation for Specific  Categories of Basic Parts=
 
(Relative to All Parts List of 8/20/07)
 
(Relative to All Parts List of 8/20/07)
  
Line 5: Line 5:
 
(8/21/07; updated 7/2/08)
 
(8/21/07; updated 7/2/08)
  
−
==Protein coding sequences (CDS’s) / Enzymes==
+
==Protein coding sequences (CDS’s) / Enzymes (CDS-E)==
  
 
ADD:
 
ADD:
  
−
Enzyme Commission (EC) number (if assigned) <SPAN style= 'color:red'>'''(1)'''</span>  
+
* E-1 Enzyme Commission (EC) number (if assigned) <SPAN style= 'color:red'>'''(1)'''</span>  
  
−
Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) <SPAN style= 'color:blue'>'''(1)'''</span>
+
* E-2 Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) <SPAN style= 'color:blue'>'''(1)'''</span>
  
−
==Protein coding sequences (CDS’s) / Repressors and Activators==
+
==Protein coding sequences (CDS’s) / Repressors and Activators (CDS-RA)==
  
 
ADD:
 
ADD:
  
−
Repressor?  ______ (yes/no).  Activator?______ (yes/no).  Both?______ (yes/no) <SPAN style= 'color:red'>'''(1)'''</span>
+
* RA-1 Repressor?  ______ (yes/no).  Activator?______ (yes/no).  Both?______ (yes/no) <SPAN style= 'color:red'>'''(1)'''</span>
  
 
''N.B.,'' Some proteins are repressors under some circumstances and activators under other circumstances.
 
''N.B.,'' Some proteins are repressors under some circumstances and activators under other circumstances.
  
−
Regulatory ligands/effectors: _____________________ (list in a box?) <SPAN style= 'color:red'>'''(1)'''</span>
+
* RA-2 Regulatory ligands/effectors: _____________________ (list in a box?) <SPAN style= 'color:red'>'''(1)'''</span>
  
−
==Protein coding sequences (CDS’s) / Reporters==
+
==Protein coding sequences (CDS’s) / Reporters (CDS-R)==
  
 
ADD:
 
ADD:
  
−
Fluorescent?  ______ (yes/no).  Luminescent?  ______(yes/no). c. Other? __________ <SPAN style= 'color:red'>'''(1)'''</span>
+
*R-1 Fluorescent?  ______ (yes/no).  Luminescent?  ______(yes/no). c. Other? __________ <SPAN style= 'color:red'>'''(1)'''</span>
  
−
Spectroscopic data:  <SPAN style= 'color:blue'>'''(2)'''</span>
+
*R-2 Spectroscopic data:  <SPAN style= 'color:blue'>'''(2)'''</span>
  
 
# absorption max. ______ nm   
 
# absorption max. ______ nm   
Line 41: Line 41:
 
Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS!  <SPAN style= 'color:red'>'''(1)'''</span>
 
Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS!  <SPAN style= 'color:red'>'''(1)'''</span>
  
−
E.C. number (if applicable)
+
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:
Line 50: Line 50:
 
nothing
 
nothing
  
−
==Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (new category)==
+
==Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (CDS-F, new category)==
  
 
ADD:
 
ADD:
Line 58: Line 58:
 
Feature annotation of the linker spanning the two fused segments  <SPAN style= 'color:red'>'''(1)'''</span>
 
Feature annotation of the linker spanning the two fused segments  <SPAN style= 'color:red'>'''(1)'''</span>
  
−
Sources of ''both'' sequences. <SPAN style= 'color:red'>'''(6)'''</span>  [Note the high point value!]
+
Sources of ''both'' sequences. <SPAN style= 'color:red'>'''(3 + 3 = 6)'''</span>  [Note the high point value!]
  
 
OMIT:
 
OMIT:
Line 112: Line 112:
 
OMIT:
 
OMIT:
 
nothing
 
nothing
 +
 +
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)