Difference between revisions of "User:Scmohr/Specialized Doc Score"
| Line 4: | Line 4: | ||
Scott C. Mohr | Scott C. Mohr | ||
(8/21/07) | (8/21/07) | ||
| + | |||
| + | ==Protein coding sequences (CDS’s) / Enzymes== | ||
| + | |||
| + | ADD: | ||
| + | |||
| + | 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> | ||
| + | |||
==Protein coding sequences (CDS’s) / Repressors and Activators== | ==Protein coding sequences (CDS’s) / Repressors and Activators== | ||
| Line 9: | Line 18: | ||
ADD: | ADD: | ||
| − | Repressor? ______ (yes/no) Activator______ (yes/no) | + | Repressor? ______ (yes/no) Activator______ (yes/no) <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. | ''N.B.,'' Both choices are necessary since some proteins are repressors under some circumstances and activators under other circumstances. | ||
| − | Regulatory ligands/effects: _____________________ (list in a box?) | + | Regulatory ligands/effects: _____________________ (list in a box?) <SPAN style= 'color:red'>'''(1)'''</span> |
| − | |||
| − | |||
==Protein coding sequences (CDS’s) / Reporters== | ==Protein coding sequences (CDS’s) / Reporters== | ||
| Line 22: | Line 29: | ||
ADD: | ADD: | ||
| − | Fluorescent ? yes/no b. Luminescent ? yes/no c. Other ? __________ | + | Fluorescent ? yes/no b. Luminescent ? yes/no c. Other ? __________ <SPAN style= 'color:red'>'''(1)'''</span> |
| − | Spectroscopic data: (a) absorption max. ______ | + | Spectroscopic data: (a) absorption max. ______ nm <SPAN style= 'color:blue'>'''(2)'''</span> |
| − | (b) emission max. ______ | + | (b) emission max. ______ nm |
| − | (c) luminescent max. ______ | + | (c) luminescent max. ______ nm |
(d) other notable spectroscopic features: _____________ | (d) other notable spectroscopic features: _____________ | ||
| − | + | ________________________________________________________ | |
| − | + | ||
| − | + | ||
| − | + | Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS! <SPAN style= 'color:red'>'''(1)'''</span> | |
| − | E.C. number | + | |
| + | E.C. number (if applicable) | ||
==Protein coding sequences (CDS’s) / Uncategorized== | ==Protein coding sequences (CDS’s) / Uncategorized== | ||
| Line 40: | Line 46: | ||
nothing | nothing | ||
OMIT: | OMIT: | ||
| − | + | nothing | |
| − | ==Protein coding sequences (CDS’s) / Fusion | + | |
| + | ==Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (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'>'''(6)'''</span> [Note the high point value!] | ||
OMIT: | OMIT: | ||
| + | |||
E.C. number(s) – if inappropriate | E.C. number(s) – if inappropriate | ||
| Line 57: | Line 67: | ||
nothing | nothing | ||
OMIT: | OMIT: | ||
| − | + | Nothing | |
| − | + | ||
==Terminators== | ==Terminators== | ||
ADD: | ADD: | ||
| − | nothing | + | nothing (best mFold structure?) |
OMIT: | OMIT: | ||
| − | + | nothing | |
| − | + | ||
==Promoters (suggested renaming of “Regulatory regions”)== | ==Promoters (suggested renaming of “Regulatory regions”)== | ||
| Line 72: | Line 80: | ||
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: | ||
| − | + | nothing | |
| − | + | ||
==RNA== | ==RNA== | ||
| − | (suggestions needed) | + | (suggestions needed!) |
ADD: | ADD: | ||
nothing | nothing | ||
OMIT: | OMIT: | ||
| − | + | nothing | |
| − | + | ||
==DNA== | ==DNA== | ||
| − | (suggestions needed) | + | (suggestions needed!) |
ADD: | ADD: | ||
nothing | nothing | ||
OMIT: | OMIT: | ||
| − | + | nothing | |
| − | + | ||
==Conjugation== | ==Conjugation== | ||
| − | (suggestions needed) | + | (suggestions needed!) |
ADD: | ADD: | ||
nothing | nothing | ||
OMIT: | OMIT: | ||
| − | + | nothing | |
| − | + | ||
Revision as of 15:29, 2 July 2008
Contents
- 1 Additional (or Modified) Documentation Required for Specific Categories of Simple Parts
- 1.1 Protein coding sequences (CDS’s) / Enzymes
- 1.2 Protein coding sequences (CDS’s) / Repressors and Activators
- 1.3 Protein coding sequences (CDS’s) / Reporters
- 1.4 Protein coding sequences (CDS’s) / Uncategorized
- 1.5 Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (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 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’s) / Enzymes
ADD:
Enzyme Commission (EC) number (if assigned) (1)
Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) (1)
Protein coding sequences (CDS’s) / Repressors and Activators
ADD:
Repressor? ______ (yes/no) Activator______ (yes/no) (1)
N.B., Both choices are necessary since some proteins are repressors under some circumstances and activators under other circumstances.
Regulatory ligands/effects: _____________________ (list in a box?) (1)
Protein coding sequences (CDS’s) / Reporters
ADD:
Fluorescent ? yes/no b. Luminescent ? yes/no c. Other ? __________ (1)
Spectroscopic data: (a) absorption max. ______ nm (2) (b) emission max. ______ nm (c) luminescent max. ______ nm (d) other notable spectroscopic features: _____________ ________________________________________________________
Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS! (1)
E.C. number (if applicable)
Protein coding sequences (CDS’s) / Uncategorized
ADD: nothing OMIT: nothing
Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (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. (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