User:Scmohr/Specialized Doc Score
Contents
- 1 Additional (or Modified) Documentation for Specific Categories of Basic Parts
- 1.1 Protein coding sequences (CDS’s) / Enzymes (CDS-E)
- 1.2 Protein coding sequences (CDS’s) / Repressors and Activators (CDS-RA)
- 1.3 Protein coding sequences (CDS’s) / Reporters (CDS-R)
- 1.4 Protein coding sequences (CDS’s) / Uncategorized (CDS-U)
- 1.5 Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (CDS-F, new category)
- 1.6 Ribosome binding Sites (RBS’s)
- 1.7 Terminators
- 1.8 Promoters (suggested renaming of “Regulatory regions”)
- 1.9 RNA
- 1.10 DNA
- 1.11 Conjugation
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)
- absorption max. ______ nm
- emission max. ______ nm
- luminescent max. ______ nm
- 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)